In the Inner Space Configuration window Game Configuration tab, under Profiles for ISBoxer EVE Launcher; for each profile I have I set Profile Inner Space Loader aggressiveness to Minimum.
So far this seems to have fixed the client loading issues. The game starts and clients are going to their respective window positions. Will continue to test.
Also, this is using the latest versions of EVE Online Launcher for ISBoxer (v1.0.0.19) and Inner Space (Build 6258).
EDIT: the other thing I did was to completely remove AVAST Antivirus, I was using the free version. Although using the game mode in the program worked before, it was completely blocking the clients from loading. At first removing this allowed the clients to load but would sometimes load into a normal window instead of where they were supposed to load until I did the above.
EDIT 2: so just an update.. I've loaded up all 14 of my toons without any further issues, so yeah.. get rid of AVAST, I've heard that the default protections by Win10 is good enough.. would love to hear any recommendations of antivirus software that is not bloated and works fine with isboxer and the eve launcher... otherwise that minimum aggressiveness setting seems to be what works best with the eve launcher.. hope this helps others