It’s seems this is a software bug.
Here is a .ZPR file [4Mb] with one simple subtool link
If you dynamesh this tool and then apply “Groups from masking” your zbrush would stuck for sure.
I try it on zbrush 4r5 and 4r6 and it stuck all the time.
I didn’t know why does this happend but it happend from time to time when i use dynamesh with different subtools.
So …
Is there is any method to avoid this error or maybe putch or something ?
Thx
I can apply groups from masking no problem

I didn’t have any problems either.

Okay. I try it at work and try it at home PC. It’s stuck.
So a bit later i will record a video. Maybe there is smal issues that i didn’t mention.
…
Here is video from my notebook lenovo i7, Geforce GT 740M.
Win7Prof x64, Zbrush 4r6.
[video=youtube_share;Q4Vx92cMCHA]http://youtu.be/Q4Vx92cMCHA[/video]
The first time I tried it, in ‘Tool > Polygroups’, I used ‘Group Masked’ and not ‘From Masking’. After seeing your video, I used ‘From Masking’ and I still didn’t have any problem. It worked like it’s supposed to. Try ‘Group Masked’ and see if you are still having the same problem. If it’s still the same, I would suggest that you start a Support ticket.
Great. Developers solve this problem in Zbrush 4R6 P2.