This post started as a request for help but ended up solving it myself so adding her in case it helps someone else. First time using CAPSMAN and now its working I really like it.

This maybe a bug? Found one post with the same issue and no answer:
Configured CAPSMAN and it was all working successfully. Rebooted the master router (RouterBOARD 962UiGS-5HacT2HnT, 6.47.9 firmware) and once it came up, nothing could connect out of 32 devices across 2.4 GHz and 3 routers. 5 GHz devices were not affected. After much checking, I found the CAP interface list under "capsman > cap interfaces" were numbered "cap1, cap2 ... cap 6" instead of the original naming convention of the AP's, this had changed post reboot. Ended up deleting the "cap1, cap2 ... cap 6" interfaces via the menu and they were automatically regenerated correctly and the issue was solved. Further reboots did not cause the same issue.

Other things learnt.
- CAPSMAN may not manage wifi on the local router unless you add the "local - local" filter rule from the bottom of the page here - https://wiki.mikrotik.com/wiki/Manual:S ... sMAN_setup
- Virtual AP's are added by using the "slave configuration" config under the provisioning tab
- Use multiple configs and "HW. supported modes" under the same provisioning menu to ensure 2.4 and 5Ghz configs are applied to the correct radio
- Alot of tutorials on the web do not mention to "forbid all" under CAPSMAN manager interfaces leaving a possible security issue (also mentioned in the above link)

Mikrotik routers are great!