Created Software Update Policies, targeted end-points, and confirmed they executed on schedule; end users were seeing a DOS / CMD Prompt window pop up during Software Update installation.
Software Update Policy's ProgramItems was being created with startWindow="Normal" and this should be created with startWindow="Hidden" which caused the popup to be thrown.
ITMS 7.5 HF1 and 7.6 HF7
Issue resolved in ITMS 7.6 post-HF7 cumulative rollup v4 outlined on INFO3457.
Note: ITMS 8.x is not affected by this issue.