Does DIFF_SYSCLK/DIFF_SYSCLK_B on the T1042 require an external termination resistor when used as an LVDS pair? The datasheet does not explicitly state it and only gives "Figure 11. LVDS receiver". AN4825 seems to show that it is internal, but this does not look to be consistent with the datasheet.
For T1042, you should treat the 100 Ω differential termination on DIFF_SYSCLK/DIFF_SYSCLK_B as internal , so you do not add another external 100 Ω resistor across the pair when the internal termination is enabled.