Second standalone taskbar not remembering size on Win 7 x64

I did open the standalone.xml file and I can see it is writing the values for the left and right coordinates, but they are negative is that correct? I would have thought it would be 0 for left and like 220 for right if the bar was on the right, but maybe that is how it should be.

Yes, negative coordinates is valid. The primary desktop always have positive coordinates, but the other desktops can have negative coordinates is they at the left side.

Please can you try to exit the standalone TLB (right-click then exit) and start it again without the rebooting. This bug looks like the second monitor is not initialized when TLB starts. So the restarting of standalone TLB only will show where the problem.