Looking at the code (LL's, not mine, i.e. all viewers react the same), an issue arises when the system time goes backwards (even by a few seconds), since the viewer code interprets it as an overflow of the time variable and "corrects" the latter to get a "valid" time delta (thus the huge difference in runtime).
This causes various issues, such as the bogus viewer stats repeated sending, but also broken animations (with "head in the ass" syndrome for avatars).
I'm currently changing the code so that such a thing won't happen (already fixed the viewer stats and "head in the ass" issues but still seeing broken anims).
So your issue would be caused by the time going backwards under Linux while the viewer has already been started.
Note that while going forward in time does not cause the same issues, it would cause a viewer spurious disconnection above 2 minutes of time shift (since that's the timeout for sim networking).
You might want to set your hardware clock to UTC (Linux works fine and is easily configurable for this mode of operation, which is the "normal" way of working for UNIX-like computers), and merge the following registry key to your Windows installation, to tell it that the hardware clock is in UTC (and should be kept that way):