Yes, transfer speed direct from the R-44 is slower than you'd expect. I don't think it's as slow as USB1 however. As the only time I have had an SDHC card fail was somewhere in the process of taking it out of the R-44 and putting it into a card reader, I now tend to do a transfer with the card in the R-44, and if that takes a little longer than via a card reader, well, it's not often those minutes would make a difference.
If you have a 12 volt battery, and set the R-44 to 9 volts, when the battery voltage goes down to or close to 9v it will assume the battery is about to go flat. I can only think that the battery isn't maintaining enough voltage under load to convince the R-44 that all is well.