'm a little confused, given the subject line of you post being about a domain transfer, while this statement is about a DNS change, and they are two different things. Changing DNS to not initiate a domain transfer and, therefore, nothing would show up in the registration section of the panel as a result of such a change. If you would share the domain name you are having trouble with, I'd love to look at the whois and other DNS information.
This sounds like a normal condition for a circumstance where you have DNS pointing to DreamHost nameservers, but have not added the domain to a hosting plan using the Control Panel -> Domains -> Manage Domains screen. Even after changing DNS, and a successful transfer, this still has to be done for the site to be "found", and content has to be placed in the appropriate directory on DH for the site to be displayed.
If you did, in fact, initiate a domain transfer in addition to changing the DNS but you have no indication of that in the panel, you probably should inquire with DH support by filing a Support Request via the control panel.
One one of my recent transfers, I also had problems with the domain not showing up as "pending transfer", and contacted support. They assured me that the transfer had been processed, and the transfer actually did occur a little later, but it never actually showed as pending. You may correct about there being some Control Panel problem with that. In your case, it almost sounds as though the transfer might be completed, but your "not found" is the result of not having added hosting to your plan for the newly transferred domain.
I'm sorry, but I didn't understand that part of you post. You might note that after changing your password in the Control Panel, it takes some time for the new password to take effect across the system; until it takes effect your old password will still work for sftp/ssh/ftp, but it will not work for the "old password" prompts in the panel IIRC , as the Panel now knows your new password (I believe, though I could be wrong on that). Again, this is probably a good thing to submit a support request about.