Hi Ionizer,
I don't use anything to copy from my windows 7 machine, I do a manual copy and that seems to work for me. I would try a manual copy just as an experiment and see if that works for you. By the way, you are using 2.02 I hope, because the earlier firmwares did not even have the alphanumeric feature working correctly. Also, which software are you using to transfer the files, is it integrated with your p2p / download or a separate item? I use something called "syncback" and that seems to work for some nas to nas backups pretty well. I am wondering if their is something incompatible with your transfer software, I know one of the other posts had trouble with the backup software they were using. That's about all I can think of right now. Good luck.
I am using 2.00 because 2.02 simply indicated it addressed two issues (3tb and time machine) which has nothing to do with what i have an issue with.
for the purposes of full disclosure, I am using a program called Alt.Binz which is nothing more than a newsgroup binary reader. It sits on my windows 7 PC, detects an NZB and downloads the data. It then proceeds to unrar it in the download folder. I then have SickBeard running which detects the final .AVI file and copies it from the Newsgroup download location to the NAS drive specific folder based on whether it's a simpsons episode, family guy, house, whatever.
Note: There is nothing special about this process. It's not really a "transfer software", it is simply performing a file move from one folder (Local drive:\blah\blah to another folder MappedNASDrive:\tv\simpsons). It's not some kind of special backup or anything else, it's just performing a move of the file. The file is verified on the nas drive, so the issue is simply that the NAS drive is not updating the index to recognize a file has been moved to it.
If I moved the file manually myself, the same issue occurs. The index is not updating automatically.
Could the index itself be broken? Is there a way to delete the index one time, generate it manually once and then hope it works fine from then on out? All of this seemed to begin breaking around the time I moved all my MP3 folders/files from my local drive to the NAS drive. That was a lot of files at once.