I had the same thing happen to me with a wifi adapter. I was using the Pi as a server to host ouimeaux (which creates a REST API to toggle Belkin wifi light switches). It worked great, except after an hour of inactivity it would take 1-2 minutes to register an action, before becoming responsive again for the next hour.

Until I properly found out how to disable wifi power saving, I worked around it by just pinging it from another device every 30 minutes to keep it awake.