When I go through some variations (Edit game mode) to the end and than back I get 'Illegal move "SOME_MOVE" (rejected by first chess program)' message and variation gets truncated after that move.
You can try to reproduce this, copy/paste this pgn data into Winboard:
1. d4 Nf6 2. c4 e6 3. Nc3 Bb4 4. a3 (4. e3 O-O 5. Bd3 c5 6. a3
Bxc3+ 7. bxc3 Nc6 8. Ne2 b6 9. e4 Ne8 10. O-O Ba6
11. f4 f5 12. Ng3 g6 $1 13. Be3 (13. exf5 exf5 14. dxc5 bxc5 15. Be3 Qa5 $11 (
15... d6 $2 16. Bxf5 gxf5 17. Qd5+)) 13... Nd6 14. exf5 $5 (14. dxc5 Nxc4 15.
Bxc4 Bxc4 16. Rf2 b5 $11) 14... Nxc4 $1 15. Bxc4 Bxc4 16. fxg6 Bxf1 17. Qh5 Qe7
18. Rxf1 hxg6 19. Qxg6+ Qg7 20. Qd3 cxd4 21. cxd4 Qh7 $1 22. Qb5 a6 $1 $15
23. Qxb6 $2 Qd3 $17) 4... Bxc3+ 5. bxc3
c5 6. e3 (6. e4 Qa5 (6... Nxe4 7. Qg4) 7.
e5 Ne4 8. Bd2 Nc6 9. Ne2 d6 10. exd6 O-O 11. Ng3 (11. f3) 11... Nxd2 12. Qxd2 Rd8 13. Ne4 cxd4 14. cxd4 Qxd2+ 15. Kxd2
f5 16. Ng5 Rxd6 $17) 6... Nc6 7. Bd3 O-O 8. Ne2 b6 9. e4 Ne8 0-1
Than on first comment window choose e3 variation and go to its end. When you get to end of variation go back one move and you should get error message and that last move will be deleted. If you than go forward and back again each last move get error message and gets truncated.
Winboard I use is master build 20101201 (from winboard 4.5.0 beta download)