I found it on this forum a long time ago, but I lost it and now I sorta need it again... How do you fix tunnels in TS (I believe it's the same in RA2).
There's apparently a bug in FinalSun that screws em up when you try to connect them and you have to go in with wordpad and fix em.
It has been discussed heavily on C-gen's (http://www.cannis.net) forums and I believe I posted a consolidated block of information into the tutorials forum on that site.