Yes. Don't use HyperTerm.
It doesn't work reliably for DNC, to be precise it doesn't wait properly for CTS. It'll only wait for so long before it sends anyway. Piece of crap, I don't know why so many people recommend it.
I guarantee that if you look closely you'll see it happening. If you turn on "Echo sent characters locally" or whatever the options called, you'll see it happily sending data, then it'll pause for the other end to catch up, then after it gets bored of waiting it'll send a character, then wait a bit again, then another character... and so on. Hence your missing characters.
Also stick to 9600 both for straight up/downloads and DNC. There is absolutely no speed advantage to anything higher because the Max II can't empty it's buffer that fast and you just end up with more/longer waits. You'll see it pausing occasionally even at 9600.
Get a decent DNC client. There are a few free ones. OneCNC NCLink is one free one that I have seen people talking about but I haven't used it myself.
Sorry I couldn't have passed this knowledge on before you learnt it the hard way!