Has anyone been able to replicate this issue?
Not me.
Is the YACoin with Coin Control still working? I would love to download it and start to use but do not know if this has been stable and developed/tested? Please let me know if there is a link with the latest build.
It's working (at least for me, and I haven't heard anyone having lost coins with the current version), but it isn't in the official branch yet. Use on own risk.
No idea about the last built, but if you can compile for your self go to github.com/saironiq/yacoin-cc.