Sometimes I like to make jam tracks to play along with by taking the drum midi and then exporting the bass to a .wav from a guitar pro tab... The problem is wav file. It exports in stereo, when imported to Sonar x3 I convert it to mono then apply a bass amp sim, if any gain or any other effects are applied they only come through the left side, clean comes through the right. It doesn't matter if I convert it to mono or leave it stereo, it's the same thing.
 
Any idea why this is happening?

Are you using POD Farm?

Yeah, not sure if that happens with any other vst though.

This is a known issue with POD Farm. Cakewalk did a fix in X3c to handle what is apparently a non-standard situation, but that created other problems so they had to revert in X3d and going forward. As a workaround, choose the Plug-In Manager, select POD Farm 2 properties, and uncheck the box for mono processing.
 
In case you're interested, Noel gave some insights into why this problem exists:
 
"Well, I spent a bunch of time investigating this one and as I suspected the issue is cloudy. I thought I'd share some  technical details about this, because it makes a good "case study" of how fragile some of this stuff is and why plugin compatibility tends to be such a complex issue. 
 
"As mentioned earlier in this thread, X3 actually deals with plugin level interleave much better than X2 or earlier in order to properly support mono only VST2 plugins, esp those that support mono sidechains such as Fabfilter and Waves stuff. In X3, SONAR specifically validates plugins for mono and stereo compatibility when the plugin is loaded. As part of this process it calls a VST2 API (called effSetSpeakerArrangement) to configure the plugin interleave. Since we test for mono and stereo, the API is called once for mono and then again subsequently for stereo. What appears to happen with PodFarm is that the call to set it to mono appears to *permanently* lock the plugin into a mono state. i.e. despite SONAR setting it to stereo subsequently it stays locked in mono. As a result the right channel is unprocessed after that point.
 
"Now whats even more interesting is that the same behavior can even be observed in X2 and earlier :)
To repro it in X2 do this:
Load  your project with a mono track feeding PodFarm on a track. Notice that the track interleave is stereo.
Now toggle the track interleave to mono and then back to stereo. 
After you do this the PodPro is stuck in mono processing mode the same way as in X3. 
 
"The only reason you see this behavior permanently in X3 is because we started calling this API at the time the plugin is loaded, to check for supported interleaves. This exposes this issue earlier on and more visibly."
 

Thanks for the info. I'll give that a go today.

Looks like that did the trick. I wonder if this will be fixed in the next version?

Don't know if you mean fixed in SONAR or POD Farm, but it was fixed in X3c. The problem was that the fix had a negative effect on other plug-ins now that SONAR offers VST3 support. So its seems a fix would have to happen at the POD Farm end of things.