This is a late reply but in case someone gets here searching the topic, I post what was my eperience.
I use the modern skin. I use a notebook. Somteimes I connect a second monitor. Last time I used Wacup I had it docked on the right side of the second monitor. When I restarted the notebook without the additional monitor, I was unable to recover the wacup window to the only monitor I had in that moment. I tried /RESETCLASSICSKINPOS and /RESETMODERNSKINPOS but no luck.
I was able to recover the situation by shutting down wacup using the taskbar or the process manager, than delete the studio.xnf file in Settings. Note that the first time I restarted Wacup, I was not able to press any menu in it. Rstarting a second time solved this issue too.
For who is interested, it seems that the rect and restoredrect settings inside studio.xnf are involved.
HTH, thx for Wacup!!