I had exactly the same problem with MailEnable 3.61 on 64bit Windows 2003 and Plesk 8.6.
The problem was that MailEnable services were running services in 64bit mode.
I ran:
sc config memtas binPath= "C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin\MEMTA.EXE"
sc config melcs binPath= "C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin\melsc.EXE"
sc config mepocs binPath= "C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin\mepoc.EXE"
sc config mepops binPath= "C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin\mepops.EXE"
sc config mesmtpcs binPath= "C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin\mesmtpc.EXE"
Before it was using binaries from C:\Program Files (x86)\Parallels\Plesk\Mail Servers\Mail Enable\Bin64\.
After that autoresponder worked just fine.