When I am mixing, I like to try out different FX while the transport is running. Lately when doing this, tracks keep falling out of sync. This causes me to have to keep either toggling the PDC button or stopping/restarting playback. Sometimes it will cause a dropout or even crash Sonar. This has gotten worse recently. Has anyone else noticed this? Is it a Sonar issue? Is it an issue with my system? Any help would be appreciated.

I've noticed that too, much more so with this update. With any DAW, it can be problematic to add things while the transport is running so I'm not really surprised. However it also seems worse with some projects than others. I haven't investigated fully, but it may have something to do with Region FX being active, or plug-ins with major lookahead for which PDC has to compensate.
 
To me it's not a big deal to have to stop, because that always lines everything back up again and that tends to be the way I work anyway...so I'm not going to roll back to a version where this is less of an issue. I do think, though, that it might be possible to isolate something that causes this to happen so that you can then avoid doing whatever that is in the future, or until there's a fix if one is needed.

Craig, I was trying out Sound Radix Auto Align (Which is an awesome program, BTW) and, in it's default mode, it was detecting everything WAYYYYYY out of sync. On their website, they have a special preset for using it with Sonar that allows proper sync. Sonar appears to be the only DAW that has an issue and therefore, it's own kludge preset. This makes me wonder what Sonar is doing that is so different from every other DAW out there?

SONAR has to calculate the delay of all plugins. SONAR cannot really calculate a plugin that is inserted during playback. Also your computer has a lot to do inserting the plugin into the random access memory - which can cause a failure during playback when your computer has a great workload (I hope google does translate this right).
Therefor stop the transport before you insert a plugin. I think that every DAW has a lot of problems when you insert a plugin during playing. And I think this is not really a problem of the DAW rather than a problem with the power of the computer  and the settings of the latency. And it is a problem how Windows can handle this.
 
For my experience SONAR syncs the tracks perfect - but if you insert a plugin during playback, the sync collapses. Then you have to close & start SONAR again.