Don't take my word for it as I'm no expert with mydns, but, mydns I believe gets it's records from the database. You should be able to find this looking through phpmyadmin easily looking as a root user in the ispconfig database. If i remember right you need to look at the soa tables records. There you will find the data that mydns is actually running off. Also you can use the dig command to interrogate your server - i think it's something like:
dig yourserver yourdomain.com
Not so much caching (although it is in a way) but if you only made a change to name servers night it can take up to 72 hours for it to propogate - and believe me it sometimes takes that long!
I hope I've understood your problem!