I have been having the same problem with the last three builds (I didn't notice it before that, so I can't say for sure it worked then either).
I have an IPOD, running the latest firmware (v1.2.6), that I formatted with MC. I have both MP3s and Monkey's Audio APE files in my library, but when I try to upload or sync the APE files it does some strange things. Here is what happens:
1 ) I right click an album and tell MC to send to Handheld
2 ) I go to upload options and check Force File Conversion with an external Lame encoder (-preset fast standard).
3 ) I upload the files and watch the decode/encode dialog bars. (BTW, It also converts regular files that are 128 kb MP3s, which is odd)
4 ) I check the file listing for my handheld in MC and the songs are listed.
5 ) I right click on my ipod in MC and "eject drive"
6 ) I wait for the "ok to disconnect" and detach the firewire cable
7 ) The songs are NOT LISTED on my ipod.
8 ) I reconnect and check MC handheld listing and the songs ARE LISTED.
9 ) I then delete the songs from my ipod and try again with the same results, and with various songs.
I have also tried this with syncing, but it will not force convert. I sent the APE files to a playlist and then tried syncing the playlist (with the upload option to convert previously checked). When it syncs, it just tries to send the APE files without converting them and returns an error.
I am running IPOD plugin version 9.0.12 and the following system setup:
Media Center Registered 9.0.146 -- C:\Program Files\J River\Media Center\
Microsoft Windows XP Workstation 5.1 Service Pack 1 (Build 2600)
AMD Athlon 1467 MHz MMX / Memory: Total - 523 MB, Free - 298 MB
Internet Explorer: 6.0.2800.1106 / ComCtl32.dll: 5.82 (xpsp1.020828-1920) / Shlwapi.dll: 6.00.2800.1106 (xpsp1.020828-1920)
Shell32.dll: 6.00.2800.1145 (xpsp2.021108-1929) / wnaspi32.dll: Internal ASPI Layer
Ripping / Drive F: Copy mode:ModeBurstBigBuffer CD Type:Auto Read speed:Max
Drive J: Copy mode:ModeBurstBigBuffer CD Type:Auto Read speed:Max
Digital playback: Yes / Use YADB: Yes / Get cover art: Yes / Calc replay gain: Yes / Copy volume: 32767
Eject after ripping: No / Play sound after ripping: No
Burning / Drive F: YAMAHA CRW3200E Addr: 1:1:0 Speed:24 MaxSpeed:24 Use MJ Engine:Yes
Test mode: No / Eject after writing: Yes / Direct decoding: Yes / Write CD-Text: No
Use playback settings: No / Normalization: None