I am having this same issue since I have updated to nxlog-ce-3.0.2272.
If you clear the configcache.dat it shutdown cleanly, however when the .dat file gets created again the problem comes back.
To my knowledge the .dat file is needed to remember the log position when reading from the event logs.
Setting CacheFlushInterval is not supported in the CE edition, so kind of stuck with a corrupted configcache.dat and cannot have the CE edition remember the log position.
Hopefully there is a fix on the horizon, I went back to nxlog-ce-2.11.2190 and the issue doesn't happen on that version.