Ahoy, Doolar...
With the issue you note, after clicking on the 'Tool Helper'.. with the pointer being offset a bit. I noted that, as well.. with CCoM, if I remember rightly..
I didn't locate a fix for it, so.. after that, I just stopped using 'Tool Helper' with those tools that were affected by the offset after opening up Tool Helper.
I know that isn't a solution that you asked for.. just letting it be known that I too, faced that issue.
Hopefully, another crops up, with a working solution to fix it, so that way.. I run into it again, will then know what to do to short circuit it from happening.
M. M.