Ok, so I don't have the solution yet, but I have some strong suspicions.
I made a Shareable CD on my hard disk from my full, production RM database. Having done so, there were 3 of 16,644 filenamess in my database that had "acquired" an additional "(2)" in the file name. I don't know why I had so few, or why I even had any. But at least I now have a repeatable way to recreate the problem.
My suspicions are now two-fold. First, I think the same thing is happening to you when you make a Shareable CD except that it's happening to a lot more of your file names than mine. I still don't know why it's happening to either one of us, so that's an item for further research. And second, after you make the Shareable CD I think you are looking at the Shareable CD version of your RM database instead of your original RM database and that's why you are seeing all the "(2)" things.
Well, there is a third option to consider, and it's even more terrible than the above. Namely, what if the ShareableCD is somehow or other getting made on top of your actual production database. I don't see how that would happen. But if it did, it could explain your symptoms. But I think it's more likely that you are looking at the wrong database.
See if any of this makes sense. Look very carefully at where your production RM database is and at where your ShareableCD database is. Hopefully, they are at different places. Then open each one separately and see what the file names look like. In addition to the "(2)" things in your file names in your Shareable CD database, you should also see a folder name of Pictures. You shouldn't see either of these things in your production RM database.
By the way, I regularly complain that RM only works with absolute file paths and then sometimes I think I remember that RM sometimes does seem to use relative file paths but I can never remember where I thought I saw RM working that way. Well, AHA! The Shareable CD works with relative file paths. You can't enter relative file paths from the RM user interface, but RM does create the Shareable CD with relative file paths. And when you run RM against the Shareable CD version of your RM database, the relative file paths are there and RM processes them just fine. Now if it would just do that all of the time, it might possibly be wonderful.
I will try to figure out what's different about my three files that have the "(2)" in the file name after a make a Shareable CD. In the meantime, please look around your disk for your production and your Shareable CD copies of your RM database as I have described above.