Avaya IP Office 412 error (Command cannot execute due to other system activity)

This is the error we are getting.  We got it for the first time yesterday, and when the system did reboot at 12am the whole configuration file was corrupted, no extensions were correct, no names, no short codes, nothing.  We were able to restore it from a .bak file however there is still some corruption, although 95% better than it was..  nothing was functional before, no incoming or outgoing calls nothing.  

Anyway trying to save another change today and we were given this same message as we got yesterday that led to the corruption.  Very worried it will happen again tonight after this reboot of the software.  Has anyone seen this?  What could be the cause / resolution?  

I ran diagnostics on the system its running on and all passed OK.   Thought it may have been hard drive going bad or something but it looks like it is OK.

Please help.

The System monitor shows this:

1999312mS PRN: WARNING:
  51999312mS PRN: The merge cannot be performed while another merge is already in progress
  51999312mS PRN:
  51999313mS PRN: WARNING:
  51999313mS PRN: The merge cannot be performed while another merge is already in progress
  51999313mS PRN:
  51999315mS PRN: WARNING:
  51999315mS PRN: The merge cannot be performed while another merge is already in progress
  51999315mS PRN:
  51999321mS CD: CALLSYNC: cs02
  51999331mS PRN: WARNING:
  51999331mS PRN: The merge cannot be performed while another merge is already in progress
  51999331mS PRN:
  51999332mS PRN: WARNING:
  51999333mS PRN: The merge cannot be performed while another merge is already in progress
  51999333mS PRN:
  51999334mS PRN: WARNING:
  51999334mS PRN: The merge cannot be performed while another merge is already in progress
  51999334mS PRN:

The system was rebooted already, same issue.  One suggestion is hard booting the avaya unit, but I am kind of afraid to do that with the issues I have been having (corruption of config etc).