This is not solved! Reading through the comments it seems that people are not listening to the real issue. The OP clearly understands that different categories give different allowances, and they have explained that they are seeing the same transactions in the SAME categories giving inconsistent results.

I'm also having this problem. 11 x Home Office costs have been disallowed. 1 is allowed.
Some Advertising / Website costs are allowed, others are disallowed.

It seems random. This is clearly a bug, or an issue with my set up, but I have filled in the limited info in the tax profile and my reports are still all incorrect.