Simply mentioned the Intel case to prompt you to see if MSI had similar requirements for your "222" board (CSM-C222-89?)... Just did a search and all the links to the detailed information about this board on the MSI site. None worked (404) - old discontinued board? Worth contacting MSI support? Maybe you already have...

ASpeed have a 'ASPEED Graphics Linux/FreeBSD/Solaris Package' available - maybe worth investigating if ClearOS is using the ASpeed SoC in the ClearOS distribution... What graphics driver is ClearOS loading? This may provide the clue as to which Graphics ClearOS is using.

when the integrated VGA on the CPU is used

Technically with the Intel Xeon E3-1200 v3 series processors the VGA graphics is provided by the Intel "222" PCH which is part of the two-chip package. Follow several CentOS forums - and never seen this type of graphics problem mentioned within those forums...Good Luck...