You must be doing something wrong. To be sure follow this instructions:
1. OPEN your .SAV in Pokesav.
2. LOAD the pokemon you want to edit into your party (loading into a box should work aswell, but I've not tried).
3. When loaded, click EDIT.
4. Go to the OT box and DELETE WHATEVER character it is between "A" and "NUB", so it reads "ANUB". Now insert a space charater using your SPACEBAR between "A" and "NUB", so it reads "A NUB".
5. Click OK.
6. SAVE your Pokemon into a .PKM file. NO NEED to save your .SAV file.
7. Open your .PKM file into a Hex Editor. Search for 01 00 (Japanese space 2 byte code). You may find it more than once, so choose the one is around the middle of the file. Replace that 01 00 and type DE 01 (correct space 2 byte code).
Example 1:
BEFORE EDITING THE .PKM FILE
00000000h: 9F 90 04 16 00 00 AD 3B 91 01 00 00 A3 2B 0B 39 ; Ÿ....;‘...£+.9
00000010h: 39 00 00 00 51 3D 00 02 00 00 00 00 00 00 00 00 ; 9...Q=..........
00000020h: 00 00 00 00 00 00 00 00 2D 00 75 00 00 00 00 00 ; ........-.u.....
00000030h: 28 0A 00 00 00 00 00 00 95 26 A8 32 00 00 00 00 ; (.......•&¨2....
00000040h: 00 00 00 00 00 00 00 00 35 01 3C 01 33 01 2D 01 ; ........5..9.>.ÿÿ....
00000060h: 00 00 00 00 00 00 00 00 4F 01 45 01 5E 01
01 00 ; ........O.E.^...
00000070h: 23 01 22 01 24 01 FF FF 00 00 00 07 05 0B 00 00 ; #.".$.ÿÿ........
00000080h: 11 00 00 01 83 02 00 00 00 00 00 00 03 00 0F 00 ; ....ƒ...........
00000090h: 0F 00 07 00 07 00 06 00 06 00 07 00 00 00 00 00 ; ................
000000a0h: 00 02 0A FF FF FF FF FF FF FF FF FF FF FF FF FF ; ...ÿÿÿÿÿÿÿÿÿÿÿÿÿ
000000b0h: FF FF FF FF FF FF FF FF FF FF 52 01 FF FF 47 01 ; ÿÿÿÿÿÿÿÿÿÿR.ÿÿG.
000000c0h: FF FF FF FF FF FF 50 01 FF FF FF FF FF FF 6A 01 ; ÿÿÿÿÿÿP.ÿÿÿÿÿÿj.
000000d0h: FF FF FF FF 00 00 00 00 00 00 00 00 00 00 00 00 ; ÿÿÿÿ............
000000e0h: 00 00 00 00 00 00 00 00 00 00 00 00Â Â Â Â Â Â ; ............
AFTER EDITING THE .PKM FILE
00000000h: 9F 90 04 16 00 00 AD 3B 91 01 00 00 A3 2B 0B 39 ; Ÿ....;‘...£+.9
00000010h: 39 00 00 00 51 3D 00 02 00 00 00 00 00 00 00 00 ; 9...Q=..........
00000020h: 00 00 00 00 00 00 00 00 2D 00 75 00 00 00 00 00 ; ........-.u.....
00000030h: 28 0A 00 00 00 00 00 00 95 26 A8 32 00 00 00 00 ; (.......•&¨2....
00000040h: 00 00 00 00 00 00 00 00 35 01 3C 01 33 01 2D 01 ; ........5..9.>.ÿÿ....
00000060h: 00 00 00 00 00 00 00 00 4F 01 45 01 5E 01
DE 01 ; ........O.E.^.Þ.
00000070h: 23 01 22 01 24 01 FF FF 00 00 00 07 05 0B 00 00 ; #.".$.ÿÿ........
00000080h: 11 00 00 01 83 02 00 00 00 00 00 00 03 00 0F 00 ; ....ƒ...........
00000090h: 0F 00 07 00 07 00 06 00 06 00 07 00 00 00 00 00 ; ................
000000a0h: 00 02 0A FF FF FF FF FF FF FF FF FF FF FF FF FF ; ...ÿÿÿÿÿÿÿÿÿÿÿÿÿ
000000b0h: FF FF FF FF FF FF FF FF FF FF 52 01 FF FF 47 01 ; ÿÿÿÿÿÿÿÿÿÿR.ÿÿG.
000000c0h: FF FF FF FF FF FF 50 01 FF FF FF FF FF FF 6A 01 ; ÿÿÿÿÿÿP.ÿÿÿÿÿÿj.
000000d0h: FF FF FF FF 00 00 00 00 00 00 00 00 00 00 00 00 ; ÿÿÿÿ............
000000e0h: 00 00 00 00 00 00 00 00 00 00 00 00Â Â Â Â Â Â ; ............
8. Save the edited .PKM file.
9. OPEN again your .SAV in Pokesav.
10. LOAD the EDITED .PKM file into your party (loading into a box should work aswell, but I've not tried). DON'T EDIT the Pokemon. I mean you can look, but don't make changes (don't press OK to close the editing window).
11. SAVE your .SAV and test how it looks within the game.
Example 2: The following pictures show how it looks the pokemon in Example 1 within the game. First picture shows the WRONG space (it is a bit wider, it is the Japanese space, resulting from just using the spacebar in Pokesav). The second picture shows the CORRECT space (using DE01 code).