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Oh, got another one! I've pasted a part of PyCharm's log this time.

2014-04-14 13:47:26,238 [ 907372] ERROR - gin.CodeivateApplicationPlugin - null
java.lang.Throwable
at com.intellij.openapi.diagnostic.Logger.error(Logger.java:92)
at com.codeivate.plugin.logic.CodeivateBusiness.run(CodeivateBusiness.java:58)
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - PyCharm 3.0.1 Build #PY-131.339
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - JDK: 1.7.0_45
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - VM: Java HotSpot(TM) 64-Bit Server VM
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - Vendor: Oracle Corporation
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - OS: Linux
2014-04-14 13:47:26,240 [ 907374] ERROR - gin.CodeivateApplicationPlugin - Last Action: DatabaseView.SynchronizeAction

I've no idea how this happened, but I had just clicked "synchronize" on my MySQL data source in the database tab.

Not sure if this is at all related, but at about this time, my internet switched over from wireless to an ethernet connection plugged into the firewall mentioned in the previous post. Before that it was running on a standard internet connection with Codeivate running fine. Just mentioning it in case this could be doing something weird.