It just happened again
$ truss -t rename -p 27999 rename(".../INBOX/cur/1368493840_0.26185.vi64-x3-2e-prg06,U=32846,FMD5=7e33429f656f1e6e9d79b29c3f82c57e:2,", ".../INBOX/cur/1368493840_0.26185.vi64-x3-2e-prg06,U=32846,FMD5=7e33429f656f1e6e9d79b29c3f82c57e:2,S") Err#2 ENOENT
$ sudo dtrace -n 'pid$target::rename:entry{ustack()}' -p 27999 dtrace: description 'pid$target::rename:entry' matched 1 probe CPU ID FUNCTION:NAME 26 109 rename:entry libc.so.1`rename mutt`maildir_sync_message+0x1b1
$ ls -l .../INBOX/*/1368493840_0.26185.vi64-x3-2e-prg06,U=32846,* .../INBOX/cur/1368493840_0.26185.vi64-x3-2e-prg06,U=32846,FMD5=7e33429f656f1e6e9d79b29c3f82c57e:2,S
In this particular case it tries to rename file to exactly the same it already is.