Why do I get the feeling that you have the server on a DHCP address? All servers, routers, gateways, etc. in your system must have fixed IP addresses, otherwise you are just begging for DNS problems. Likewise, all users need to point to the internal DNS first, then to external DNS resources.
Adding an ISDN Internet access point should not change your network. Did you get a new range of fixed IP addresses when you changed to the ISDN system? Does you local DNS correctly reflect these new addresses?
I can not understand why you must have the ISDN modem be the DHCP server for your network. Your local DNS/DHCP server should be handing out the ISDN port IP address as the gateway for all the users, as that is all a stand alone ISDN modem should be as far as the network is considered.
What all did you have to change when you made the ISDN modem your DHCP server? I would revert back to the original configuration, add the ISDN as the gateway, and continue to march.
Your system should work without the ISDN active at all, and it sounds like you have made the ISDN modem the single point of failure in your system, instead of just being a gateway to the world. Does the ISDN Modem terminate in its own box with a hub connection, or is it on a card in the server? In the first case, simply attach it to your network, assign a local address for the modem to be the gateway address for the network, have your local DNS/DHCP server hand out the "gateway" address, and you should be off and running.
In the second case, the ISDN card becomes a net card in the server. This net card should then be the only card in the server with a gateway address. All other local users will need to point to the server network side card as a gateway address, and you need to turn the IP relay function on in the server so it will pass the outbound traffic to the ISDN card and route incoming traffic back to the internal network.
The long load time looks like a DNS issue. Make sure all the DNS information being provided in the DHCP give the users the local DNS server address first, then the Internet DNS server address second and third, otherwise everyone will go out to the Internet and get routed back to the local DNS for every lookup. In addition, your local DNS MUST point to itself first in the DNS look up configuration, or it will not know where to go to look itself up!
The profile loading issue says the users are having a hard time finding the Profile server (DNS issue!) OR else the users just have LARGE Profiles! For your roaming profiles I would recommend putting the users home directory on the server so all the doc files, etc., do not get downloaded to whatever system a user logs on to each time they log on. I would suspect the first case if it worked fine before changing the configuration.
HTH
David