Re-encoding MKV AAC to MKV AC3 causes a delay

[VideoFanatic]

Here's my FFMPEG script:

"X:\Portable Installations\ffmpeg-2014 May 14-git-72dcd48-win64-static\bin\ffmpeg.exe" -i %1 -c copy -absf aac_adtstoasc -vn gain.m4a
"X:\Portable Installations\AAC Gain 1.9\aacgain" -r -k -m 0 gain.m4a
"X:\Portable Installations\ffmpeg-2014 May 14-git-72dcd48-win64-static\bin\ffmpeg.exe" -i gain.m4a -acodec copy "%~d1%~p1%~n1.aac"
"X:\Portable Installations\ffmpeg-2014 May 14-git-72dcd48-win64-static\bin\ffmpeg.exe" -i %1 -i gain.m4a -map 0:v -map 1 -c:v copy -c:a ac3 -ab 2 -ab 128k "%~d1%~p1%~n1.AC3.mkv"
del gain.m4a
"X:\Daves Folder\Sounds\VideoRedo Completed Sound Short.WAV"
pause

I put the above batch file in the "Send To" directory in Windows, I right-click a video, select Send TO then select the batch file and it does the following: Muxes MKV to MKV and re-encodes AAC to AC3. It also demuxes the AAC in the MKV into an AAC file and normalizes both the AAC and AC3!

The problem is that the MKV output by FFMPEG has a 1 minute 5 second delay. There's no audio for the first 1 minute 5 seconds and I can see the delay mentioned in MediaInfo. How can I prevent FFMPEG from causing a delay?