I keep turning off sympathetic highlighting in all my bibles. When I reload Logos the sympathetic highlighting is back on. It seems to stick within a Logos session i.e. when I've changed layouts, then go back to the earlier layout, but not when I've fully exited the program.
I had the same problem in Beta 4.

HP Pavilion dv7 Notebook PC, x64-based, AMD Turion X2 Dual-Core Mobile RM-72, MS Windows Vista Home Premium.