I am 99.9% sure the card simply does not have fully KS 1.3 compatible setup and has nothing to do with ACA500. KS 1.3 has really strict HD filesystem requirements compared to KS 2.0+. (Setting up HD under KS 1.3 is also quite annoying, much easier under KS 2.0+)
Size of card? Size of partitions? Dostype of partitions? RDB installed filesystem version? (Any even slightly wrong and there will be trouble under KS 1.3)
I'd of course recommend PFS3AIO
EDIT: I use ACA500 for transferring data between PC and Amiga (mainly for emulation comparison purposes) using FAT formatted CF card and PFS3AIO formatted CF card, it works perfectly under KS 1.3.