Since you are on a PC, you should try dBpoweramp for your conversions. It will let you do the conversion in one step to just about any format. I store all my masters in FLAC and then convert as required.
You didn't mention how you were coming out of the iPad (headphones, FM transmitter, etc.), that could be much more of a problem than just file format.
Also, as of about 2-3 days ago the new VLC Media Player for iPad is available as a free download. It plays almost all video and audio formats. I haven't tried it on FLAC but I'll bet it works. It's a "must have" for video on the iPad.
Paul
You didn't mention how you were coming out of the iPad (headphones, FM transmitter, etc.), that could be much more of a problem than just file format.
Also, as of about 2-3 days ago the new VLC Media Player for iPad is available as a free download. It plays almost all video and audio formats. I haven't tried it on FLAC but I'll bet it works. It's a "must have" for video on the iPad.
Paul