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I would first see if your Kindle is having a problem indexing your content, by searching for '.' (period). This should return no search results, but it will tell you if there are 'unindexed items'. Normally this queue gets processed and cleared out, but if one of your items is corrupt, or has a DRM key that doesn't correspond to your Kindle, indexing will get stuck, and suck CPU cycles, and searches will be unreasonably lengthy. The solution is to identify the item that it's stuck on and eliminate it (might require tethering to computer to do this).
A related issue is that if you do a lot of bookmarks, highlights and notes, 'my clippings.txt' can get very large. Each time you add another one of these things, Kindle has to re-index my clippings, and the time it takes to do that is proportional to the size of the file. Again, it takes CPU cycles, slows down everything else.
Finally it might be a problem with the index files themselves. There's simple a way to delete them and start over, but I don't know the details off hand. google 'kindle reindex' or something like that and it should show up in the search results.
I doubt it has to do with your Collection names, which are stored in files that are not indexed for search.
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