Yeah, I've had problems in the past with importing the v3 PGN into a program. The ones from v2 work great. I can also import the v3 version into my database program, without issue, export that and import into the offending program.
They changed something in the formatting of the export between versions. Not exactly sure what but maybe how they encode line returns? I haven't tested recently but based on your comment, I don't think it will works still.
I have noticed that Fritz 14 seems to be experiencing difficulty importing PGN generated by Chess.com 3.0 into its program. Here is what is going on:
I recently completed a Chess960 game and downloaded the PGN file. When I open the file with Notepad, I find something like this:
[Event "Let's Play!"][Site "Chess.com"][Date "2015.03.18"][White "RooksBailey"][Black "X"][Result "1/2-1/2"][WhiteElo "1533"][BlackElo "1510"][TimeControl "1 in 14 days"][Termination "Game drawn by agreement"][Variant "Chess960"][SetUp "1"]
[FEN "nbbqrknr/pppppppp/8/8/8/8/PPPPPPPP/NBBQRKNR w KQkq - 0 1"]
[CurrentPosition "8/8/8/p1pB4/P4kp1/1P6/6K1/4b3 b - - 0 45"]1.c4 d5 2.cxd5 Qxd5 3.Nf3 c6 4.d4 Nf6 5.O-O Bg4 6.Nb3 Qh5 7.h3 Bxf3 8.exf3 O-O 9.Nc5 b6 10.Ne4 Nc7 11.Nxf6+ exf6 12.Rxe8 Rxe8 13.Re1 Re6 14.g4 Qxh3 15.Bf4 g6 16.Bc2 Rxe1+ 17.Qxe1 Qxf3 18.Bxc7 Bxc7 19.Qe4 Qxe4 20.Bxe4 c5 21.dxc5 bxc5 22.Bd5 Kf8 23.f3 Be5 24.b3 Ke7 25.Kg2 f5 26.Kh3 fxg4+ 27.Kxg4 f6 28.a4 a5 29.Bc4 h6 30.Bd3 f5+ 31.Kh4 Kf6 32.Bc4 h5 33.Bd3 Bf4 34.Bc4 Kg7 35.Be6 Kh6 36.Kh3 g5 37.Bxf5 Kg7 38.Kg2 Kf6 39.Be4 g4 40.fxg4 hxg4 41.Kf2 Bd2 42.Kg3 Kg5 43.Bc6 Be1+ 44.Kg2 Kf4 45.Bd5 1/2-1/2
Notice how it all runs together.
When I put it into Fritz 14, Fritz gets confused and outputs this:
[Event "Let's Play!"]
[Site "Chess.com"]
[Date "2015.03.18"]
[Round "?"]
[White "RooksBailey"]
[Black "X"]
[Result "1/2-1/2"]
[WhiteElo "1533"]
[BlackElo "1510"]
[SetUp "1"]
[FEN "nbbqrknr/pppppppp/8/8/8/8/PPPPPPPP/NBBQRKNR w - - 0 1"]
[PlyCount "14"]
[EventDate "2015.??.??"]
[TimeControl "1"]
1. c4 d5 2. cxd5 Qxd5 3. Nf3 c6 4. d4 Nf6 {O-O Bg4} 5. Nb3 Qh5 6. h3 {Bxf3
exf3 O-O Nc5} b6 {Ne4 Nc7 Nxf6+ exf6 Rxe8 Rxe8 Re1 Re6} 7. g4 Qxh3+ {Bf4 g6
Bc2 Rxe1+ Qxe1 Qxf3 Bxc7 Bxc7 Qe4 Qxe4 Bxe4 c5 dxc5 bxc5 Bd5 Kf8 f3 Be5 b3 Ke7
Kg2 f5 Kh3 fxg4+ Kxg4 f6 a4 a5 Bc4 h6 Bd3 f5+ Kh4 Kf6 Bc4 h5 Bd3 Bf4 Bc4 Kg7
Be6 Kh6 Kh3 g5 Bxf5 Kg7 Kg2 Kf6 Be4 g4 fxg4 hxg4 Kf2 Bd2 Kg3 Kg5 Bc6 Be1+ Kg2
Kf4 Bd5} 1/2-1/2
Notice how it thinks ply 5 is a variation (it puts it in brackets), something that throws off the rest of the numbering. By ply 8, the entire game is now one numberless variation!
But this is what happens when I download the same PGN from the old Chess.com 2.0 website:
[Event "Let's Play!"]
[Site "Chess.com"]
[Date "2015.03.18"]
[White "RooksBailey"]
[Black "digitalAtrophy"]
[Result "1/2-1/2"]
[WhiteElo "1533"]
[BlackElo "1510"]
[TimeControl "1 in 14 days"]
[Termination "Game drawn by agreement"]
[Variant "Chess 960"]
[SetUp "1"]
[FEN "nbbqrknr/pppppppp/8/8/8/8/PPPPPPPP/NBBQRKNR w KQkq - 0 1"]
1.c4 d5 2.cxd5 Qxd5 3.Nf3 c6 4.d4 Nf6 5.O-O Bg4 6.Nb3 Qh5 7.h3 Bxf3 8.exf3 O-O 9.Nc5 b6 10.Ne4 Nc7
11.Nxf6+ exf6 12.Rxe8 Rxe8 13.Re1 Re6 14.g4 Qxh3 15.Bf4 g6 16.Bc2 Rxe1+ 17.Qxe1 Qxf3 18.Bxc7 Bxc7 19.Qe4 Qxe4 20.Bxe4 c5
21.dxc5 bxc5 22.Bd5 Kf8 23.f3 Be5 24.b3 Ke7 25.Kg2 f5 26.Kh3 fxg4+ 27.Kxg4 f6 28.a4 a5 29.Bc4 h6 30.Bd3 f5+
31.Kh4 Kf6 32.Bc4 h5 33.Bd3 Bf4 34.Bc4 Kg7 35.Be6 Kh6 36.Kh3 g5 37.Bxf5 Kg7 38.Kg2 Kf6 39.Be4 g4 40.fxg4 hxg4
41.Kf2 Bd2 42.Kg3 Kg5 43.Bc6 Be1+ 44.Kg2 Kf4 45.Bd5 1/2-1/2
Notice how it is properly formatted in Notepad? And when I copy and paste it into Fritz 14, it correctly reads the PGN:
[Event "Let's Play!"]
[Site "Chess.com"]
[Date "2015.03.18"]
[Round "?"]
[White "RooksBailey"]
[Black "X"]
[Result "1/2-1/2"]
[WhiteElo "1533"]
[BlackElo "1510"]
[Variant "chess 960"]
[SetUp "1"]
[FEN "nbbqrknr/pppppppp/8/8/8/8/PPPPPPPP/NBBQRKNR w HEhe - 0 1"]
[PlyCount "89"]
[EventDate "2015.??.??"]
[TimeControl "1"]
1. c4 d5 2. cxd5 Qxd5 3. Nf3 c6 4. d4 Nf6 5. O-O Bg4 6. Nb3 Qh5 7. h3 Bxf3 8.
exf3 O-O 9. Nc5 b6 10. Ne4 Nc7 11. Nxf6+ exf6 12. Rxe8 Rxe8 13. Re1 Re6 14. g4
Qxh3 15. Bf4 g6 16. Bc2 Rxe1+ 17. Qxe1 Qxf3 18. Bxc7 Bxc7 19. Qe4 Qxe4 20. Bxe4
c5 21. dxc5 bxc5 22. Bd5 Kf8 23. f3 Be5 24. b3 Ke7 25. Kg2 f5 26. Kh3 fxg4+ 27.
Kxg4 f6 28. a4 a5 29. Bc4 h6 30. Bd3 f5+ 31. Kh4 Kf6 32. Bc4 h5 33. Bd3 Bf4 34.
Bc4 Kg7 35. Be6 Kh6 36. Kh3 g5 37. Bxf5 Kg7 38. Kg2 Kf6 39. Be4 g4 40. fxg4
hxg4 41. Kf2 Bd2 42. Kg3 Kg5 43. Bc6 Be1+ 44. Kg2 Kf4 45. Bd5 1/2-1/2
So...what changed between Chess.com 2.0 and 3.0 when it comes to PGN? The only obvious differences I see are a) the formatting, and b) the addition of a [CurrentPosition] tag. However, when I delete that tag, the PGN still reads incorrectly.
I am a bit confused by this.
Could we have the PGN set back to the 2.0 version? Entering a lengthy game by hand into Fritz is going to get annoying really quickly. 
Either that, or please correct whatever is messing with the new PGN output file.
Thanks!