A few different things that could be causing this:
1.) Clients aren't able to upload their logs to the SEPM due to something blocking the communication, either at a network level (like a proxy or firewall) or a configuration level (like someone changing the IIS configuration in some fashion).
2.) Clients might be updating from LiveUpdate rather than the SEPM, giving the illusion that the communications are only broken for the download...would depend on how the LiveUpdate policy is configured.
3.) The SEPM may be under-resourced and isn't able to keep up with the log processing, or there's a broken log jamming up the works...how many files are in C:\Program Files\Symantec\Symantec Endpoint Protection Manger\data\inbox\agentinfo and \data\inbox\client? Is it a relatively small amount, or is it several thousand? If you wait a few minutes then check again, is the number relatively the same, or is it growing?
I'd recommend gathering a sylink log and checking those two folders to help give us an idea as to where the communication breakdown might be. Here's a link to the document on creating a sylink log:
http://www.symantec.com/business/support/index?page=content&id=TECH104758