The problem is that the logic uses to calculate the subtotal excluding tax in the line item is adding up all line items except tax and subtotal. This used to work fine until now but I just defined a line item with calculated => FALSE (as subtotal and total) and it only got added to the subtotal excluding tax line. The reason is that this property is not queried properly in the logic.
For reference, you can see uc_line_items_calculate().
It took me a while to get to this. Even more because I use uc_vat and that module overrides a few functions but borrowed the same logic into it.
The patch I will submit I haven't been able to test it myself properly, because I tested the same patch for uc_vat, but I'd think it's pretty simple and it should definitely work.
PASSED: [[SimpleTest]]: [MySQL] 2,146 pass(es).
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch 644840_proper_line_item_logic_in_subtotal-2x.patch. This may be a -p0 (old style) patch, which is no longer supported by the testbots.
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch 644840_proper_line_item_logic_in_subtotal.patch.