309 is the correct latest "release" version.
What are these wav files that are so short? You might be trying to do something that MC was never designed to, or of coarse this may be an area no one has tried before, (very short files), and therefore may need some tweaking.
I don't think I've ever played a file shorter than 7 or 8 seconds in the 3 years I've been using MC and so have never come across this issue.
Unfortunately this is the weekend, so the JRiver team may not see this until monday, but maybe one of the "Beta" testers will help out.
As very few users run MC with default settings, I doubt that even the JRiver has those defailt settings memorized, so it always helps and saves time to list all relevant data that describes how a person uses MC. The more information one supplies, the more helpful the "brain trust" here can be.
There were some major changes between v10 and v11, so there are still a few small bugs to be worked out. It may be a big bug to you, but compared to the total development picture... , but I assure you that every issue is looked at.