2015/06/11 20:47:50.895 [1396:2464] GUProxy - Error: FreeCacheEntry called on an entry in use
From the log, it looks like the cache size might occationally be getting full, preventing the GUP from downloading new updates requested by the clients.
If your clients are set to download the updates everyday (once or several times), then change the following setting in the live update policy.
Delete content update if unused = 2 days.
Note: Do not confuse the above settings to the number of content revision kept by the SEPM. The GUP simply download the definitions requested by the clients and keep a copy of it in the "SharedUpdates" folder to serve request, if any, for same file in future. The GUP doesn't have the ability to merge definitions or to create delta definition. As a client (which is communicating with SEPM) will try to download only the latest definition available with SEPM, keeping the older definitions on the GUP is unnecessary and waste of space on the cache.
Maximum disk cache size for content updates = 4096
Note: As now-a-days the size of 1 full definition is around 1 GB. Hence keeping enough space to accomodate atleast 2 Full definitions and some delta definitions is necessary.
Also, consider keeping as many definition as possible in the SEPM server.