Relace the relevant parts of your INI with these, and see how you go. NOTE: I have set Debug to 1 for now, so you can check what's happening (if anything...).
This is untested. It is, at least, a start though.
[Settings]
Config=APE
EAC=C:\Program Files\Exact Audio Copy\EAC.exe
musicdir=E:\music
encdir=E:\soft\audio
LogFile=react.txt
CodePage=1252
MinimizeCompressionWindow=1
ProcessPriority=1
ImageHotkey={F10}
ImageNaming=$artist$ - (@year@) $album$
KeyRemap1={F4}|+{F5}
KeyRemap2=|
KeyRemap3=|
Sla_Bks_Col_Qst_Bar_Quo_Ast_Lt_Gt=-|-|-||!|'|#|[|]
Version=0.996
Debug=0
[APE-tracks]
Description=Monkey's Audio, MP3, and MPC
destdir1=@musicdir@\$cdartist$\$album$\APE
destdir2=@musicdir@\$cdartist$\$album$\MP3
destdir3=@musicdir@\$cdartist$\$album$\MPC
dest1=@destdir1@\$artist$ - $album$ - $track$ - $title$ - $year$ - $genre$
dest2=@destdir2@\$artist$ - $album$ - $track$ - $title$ - $year$ - $genre$
dest3=@destdir3@\$artist$ - $album$ - $track$ - $title$ - $year$ - $genre$
Various-dest1=@destdir1@\$album$ - $track$ - $artist$ - $title$ - $year$ - $genre$
Various-dest2=@destdir2@\$album$ - $track$ - $artist$ - $title$ - $year$ - $genre$
Various-dest3=@destdir3@\$album$ - $track$ - $artist$ - $title$ - $year$ - $genre$
1=>"@encdir@\monkeysaudio\Monkey's Audio\MAC.EXE" "@source@" "@dest1@.ape" -c3000
2=>@encdir@\musepack\TAG.EXE --ape2 -t "ARTIST=@artist@" -t "ALBUM=@album@" -t "TRACK=@track@" -t "TITLE=@title@" -t "YEAR=@year@" -t "GENRE=@genre@" "@dest1@.ape"
3=>"@encdir@\razorlame\LAME.EXE" --alt-preset standard --ta "@artist@" --tt "@title@" --tl "@album@" --ty "@year@" --tn "@track@" "@source@" "@dest2@.mp3"
4=>"@encdir@\musepack\MPPENC.EXE" --braindead --xlevel --artist "@artist@" --title "@title@" --album "@album@" --year "@year@" --track "@track@" --genre "@genre@" "@source@" "@dest3@.mpc"
5=>MOVE "@source@" "@dest1@.wav"
6=>IF @islast@==0 GOTO End
7=>MOVE "@eaclog@" "@destdir1@\EAC_log.txt"
8=>DEL "@destdir1@\*.wav"
9=>:End