I have two problems.
1. Whenever I open my already working fine website and save in JMS2Win Multisite settings in websites tab, my Slave website gives "Internal server error", no solution, then I reverted to my full backup of 20 ago of my hosting account.

2. Second problem is very very big. This is as following:

I am suffering from a very very strange problem on my website.

My website URL is globaljournals.org/ (You might remember you provided me telephonic support once)

After some time (may be within 2 or 3 hours) after I cleaned my cache of joomla, All menu links becomes 404 (link becomes completely different and contains rss word also etc etc automatically).

Then I uninstalled all rss related components, plugins etc. from my joomla.
Problem is now also but now rss is not in BAD urls that are generated
eg now it is like this:
globaljournals.org/index.php/research/Li...nu-id-158?Name=Value


Please note that it must not include /index.php/research/Library/subscription/GJPortal/Visibility/visibility/rss/reader/for-individual/privacy-policy/Fellows/fellowsmembers-of-global-journal-of-computer-science-and-technology/. Correct URL (after whenever I clear my cache) is short also with no 404

Again when I clear cache, everything starts working fine again. But, after 1 or 2 or 3 hours again links become 404 type.

I really don't know why this is happening.

What I already tried:
1. Updated roknav menu to its latest versio.
2. Updated and reinstalled sh404sef, akeeba admin tools and JMS2Win Multisites to their latest version.
3. Tried htaccess settings change in global configuration
4. checked complete htaccess kind of things
5. Updated Gantry
6. Uninstalled and deleted all rss related things from my joomla
7. many times tried with different browsers and cache deletion
8. Tried to visit nearly every page to diagnose why this is happening.
9. Uninstalled everything related with rss before that rss was included and now rss word is now not coming in URL
10. Updated Joomla
11. Tried to disable JCH optimize etc.
12. Purge URLs
13. Extensions > Plugin manager > search for "System - Cache" click on it and at "Oder:" field make sure it`s set to LAST
14. Disabled Rok gantry cache
15. Disabled caching and expiration from htaccess
16. Disabled use of htacess for optimization in JCH Optimize
17. Disabled use of Google AJAX files
18. Disabled Mootools upgrade plugin
19. "Add suffix to URL" is disabled
20. roknavmenubundle in sh404sef to skip
21. Website FULL WEBSITE BACKUP RESTORE TO 20 DAYS AGO. STILL NO LUCK.
22. Uninstalled K2
23. Disabled Google AJAX files
24. I have tried disabling sh404SEF and purging urls. Cleared cache and still had problems.
25.I then disabled the Joomla SEF and Rewrite in global config. Still had problems.
26. Uninstalled sh404sef and rss plugins and components from Slave websites
27. Updated Joomla to latest

What I still not tried:
1. Re-installing template as there are some minor customization in template which are working very fine since many months

Website was working fine since 2 weeks ago. I dont remember when and why problem started exactly.

Please help me. If you need backend access then kindly let me know the method by which I can tell you details.

Similar closed topic you can see here:

Extra notes (PLEASE NOTE THAT EVERYTHING WAS WORKING FINE SINCE MANY MONTHS WITH FOLLOWING AND CONFIGURATION OF FOLLOWING ARE STILL UNTOUCHED):
1. I am using custom htaccess generated by Akeeba Admin tools
2. This is a master website

############## System Details ##############
PHP Built on: Linux gator157.hostgator.com 2.6.38.7 #9 SMP Tue Aug 16 03:06:42 CDT 2011 i686
Database Version: 5.1.56
Database Collation: utf8_general_ci
PHP Version: 5.2.17
Web Server: Apache mod_fcgid/2.3.6 mod_auth_passthrough/2.1 mod_bwlimited/1.4 FrontPage/5.0.2.2635
Server PHP interface: cgi-fcgi
Joomla! Version: Joomla! 1.5.24 Stable [ senu takaa ama naiki ] 17-October-2011 18:00 GMT
User Agent: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.835.202 Safari/535.1
sh404SEF Version: 2.3.0.988

You can also refer to following two threads:
www.rockettheme.com/forum/index.php?f=38...9&rb_v=viewtopic

and

anything-digital.com/forum/extension/sh4...-clearing-cache.html

In both of above they are saying that this there may be problem because of JMS2WIN.

1) Internal Server Error might be due to permission error.
See your server error log to have more information on the reason of the "Internal Server Error".
For example if suPHP is installed and that you have a directory with 777, this return an "Internal Server Error".

2) Most of the RSS plugin perform call to the server with the "port" number present in the URL.
So you also have to define the website the port in the URL.
ie. domain.com:80/index.php....

You seems also report a cache problem that is perhpas due to a wrong domain or subdomain "document root" definition that you did on your server.
When you mentioned cache, you didn't specified which kind of cache.
Do you use specific SEF extension that would save URL in a cache or do you user specific extension to manage the cache or specific joomla template that include a cache, ....

You mentioned also that you are using sh404SEF but didn't mentioned the version.
All we know is that recent version of sh404SEF have bugs. So if you have problem with sh404SEF cache or URL processing or whatever, we suggest that you report such issue to sh404SEF

When you mention "latest version", please write explicivelly the version number.

Concerning sh404SEF, you mentioned a version 2.3.0.988 the only know issue under joomla 1.5 is that the configuration is shared between the website. This issue is fixed and will be available in next release of JMS 1.2.72 to apply the same fix as for joomla 1.7.

Concerning the RT thread we don't have access.
Concerning the other thread to sh404SEF, this is good to have them know the issue.

As you mentioned that you had the website working for several month and this is something that is happen recently, perhaps you could check the directory date and time to remember what you changed recently and perhpas identify which extension is at the origin of the issue.

I think you are using hostgator shared hosting.
Perhaps that you have enabled the error log traces to keep history of the access.
If this is the case, perhaps you still have 1 month history and that you could identify the date when the problem start to occurs and perhaps identify what you did at this time.

Based on what you described, it seems this is an update of an extension.
The 404 error seems more related to sh404 than to RT.