Can you give us the example of error message that you received.
Perhaps a screenshot will help us.

The test that we did and that was OK is the following.
We installed JCE in the master website.
After that we installed the "template manager" in the JCE AddOn plugins.

When done, we replicated the master website to create a slave site with a specific images directory. In JMS Template rule, we selected "copy" action for the "/images" directory.
In this case, the "template manger" button present in the article display the correct list of files and folder corresponding to the slave site.

If you had decided to share the "/images" directory with "Symbolic Link" in the JMS Template rule then you have the same "/images" directory and therefore the template manager display the same files and folders.

So if you have additional info on the scenario that would help us to reproduce the behavior, they are welcome. (screenshot, step by step procedure, ...)

I will try to get the detailed info this weekend.
The basics are:
I have a master site and about 10 slave sites. All of which have their own Template folder and their own Images folder. I've installed the JCE plugin on the Master site, and the slave sites. I've also installed the JCE add-on on the Master site and the Slave site. When clicking the icon on the Master site I get the Template window as expected. When clicking on the template icon on the Slave site the little html popup "window" starts to load but the content is "squished" down to the bottom by the following error Messages...
Warning: array_merge_recursive() [function.array-merge-recursive]: Argument #1 is not an array in /home1/dataload/public_html/mastersite/components/com_jce/editor/libraries/classes/editor.php on line 247

Warning: Invalid argument supplied for foreach() in /home1/dataload/public_html/mastersite/administrator/components/com_jce/classes/parameter.php on line 312

Warning: array_merge_recursive() [function.array-merge-recursive]: Argument #1 is not an array in /home1/dataload/public_html/mastersite/components/com_jce/editor/libraries/classes/editor.php on line 247

Warning: Invalid argument supplied for foreach() in /home1/dataload/public_html/mastersite/administrator/components/com_jce/classes/parameter.php on line 312

Warning: array_merge_recursive() [function.array-merge-recursive]: Argument #1 is not an array in /home1/dataload/public_html/mastersite/components/com_jce/editor/libraries/classes/editor.php on line 247

Warning: Invalid argument supplied for foreach() in /home1/dataload/public_html/mastersite/administrator/components/com_jce/classes/parameter.php on line 312

(note: I changed the name of my master site in the path above to "mastersite" to try and protect my site.)

The error line 247, seems related to a bad value in the configuration of JCE.
Perhaps you have put a wrong value somewhere.

The error seems related to a wrong value provide to the json_decode function and that would return a bad value.

I suggest that you report this issue to JCE support.

The second warning in line 312 is the consequence of the previous one.