Please correct me if I misunderstood. Are you using conditional format in the matrix and then finding that they are not aligned properly according to the rules? Can you provide a screenshot of the sample (without sensitive information) so that we can better help you troubleshoot the problem?
Did I miss something? How do I reproduce your question correctly? I made two separate simple samples, one with a custom background color, and when I publish to Power BI Service, it works fine.
I have the same issue with my reports and I've noticed that the issue only arises when the Row Subtotals are set to On and a custom Background colour is selected for the subtotal.
it's when subtotals are on that causes the issue. I do want to point out that this was not a problem in the past 2 years. This is a new problem just starting on Monday.
Thanks to the useful information provided by all of you, we have reproduced the issue and submitted it to internal ICM 298830938, engineers are doing their best to fix this issue, please be patient and I will give you feedback here once there is any progress.
After testing, the issue has now been fixed.