I use mouse 3 (thumb, not middle) as an alternate button for shift functions in this, and if I'm holding down left mouse to guide my fleet through a storm I can't begin to accelerate time unless I let go of the button, or in combat start to turn to cursor if I'm firing weapons. It only stops the detection of click down; it will stay detecting if I click 3 before LB and hold or release. The mouse is reporting this fine to other programs, so it's not just a hardware issue.
Example input sequences:
LB down, M3 down, LB up, M3 up: Fires weapons, never turns to cursor.
M3 down, LB down, LB up, M3 up: as expected, turns to cursor, fires, stops turning to cursor
M3 down, LB down, M3 up*, M3 down, LB up, M3 up, M3 down^: Stops turning to cursor at *, doesn't resume again until ^
LB down, Shift down, M3 down, Shift up*, LB up, M3 up: Stops turning to cursor at *
Just tested, same behavior with 3 and right button, too.
Possibly related, more minor: I use mouse wheel left/right for volume up/down, and that toggles weapon arcs as if I had hit `. Volume up/down are not set as alternate buttons for that.