I have the problem of Time Machine finding too many files it thinks need to be backed up, running OS 10.9.1. I had the same problem with a prior OS as well, on a different macbook pro, with a different external harddrive.
The console reports that it found > 100,000 files needing to be backed up. Ultimately, it may back up only 200 files.
The only way I have found to address it (now under 10.9.1 or a few years ago under an earlier OS, machine, and external drive) is to place the no_log file in /.fseventsd.
That seems to solve it every time.
If I delete that directory, and restart the machine, the first few backups operate normally. But, over time (a day or sometimes less), the problem eventually returns. And, the return isn't gradual - I'll have a series of backups that happen normally - time machine finds a few hundred files to back up and then actually copies some number close to the value reported in the "Found X files () needing backup" log message.
But, then one backup will suddenly find > 100,000 files needing backup. And, it just grows from there. It never actually backs up that many files, so I can't determine which files it thinks it needs to backup.
I haven't identified anything that I'm doing that is unusual between the normal backups and the first abnormal backup.
I don't know what the effect of not logging in .fseventsd. But, spending > 10 minutes trying to back up a few MB to a directly connected thunderbolt drive because it's spending 10 of those minutes apparently finding files that it doesn't end up copying is unaceptable.
If there a way to get a listing of the files that it thinks need to be backed up (as reported in the "Found X files () needing backup" messages? If I could get that list, I'd have some chance of trying to debug this.