I started having a similar problem with logs not uploading. Looking at my logs.tf uploads page, the timing seems to coincide with the Invasion update. The latest entry with "0 players" under "format" is a test after I attempted a fix, which I explain below.

I determined this fix by examining a log file located at tf/addons/sourcemod/logs/errors_20151019.log. I've uploaded it using sprunge: http://sprunge.us/YPTP

I noticed a lot of errors coming from supstats2.smx. The first instance of one of these errors can be found at 20:42:35 in the log file. The error where the logs fail to upload can be found at 20:42:35.

I disabled supstats2.smx, then tested it by executing some UGC HL configs with another guy in the server. We finished two rounds, and the stats successfully uploaded like they used to.

Some things to note:

1. There are more recent logs than this that do not have any errors related to supstats2.smx, yet we've since had matches where the logs fail to upload. This makes me think that supstats2.smx may not actually be the culprit, although my test may indicate otherwise.
   
2. Looking at that same log file, it also looks like this was before I updated SourceMod. This might explain my previous point about supstats2.smx not reporting any errors since that day.
   
3. This was a quick test done with just two players. We have Highlander matches scheduled for tonight where a more proper test can be performed, although I'm not sure the results will differ depending on the number of players in the server. I'll post an update after our matches tonight on whether or not the logs upload.

EDIT: So the logs uploaded after one of our scrims tonight, but none of the information was accurate. I've had this problem before and was never able to figure out what was causing it. But it does seem to be a different issue.