Applicants complained of referees being unable to complete their sections, course names and codes not matching, and forms being sent in late to universities and colleges.
Others were unable to track the progress of their applications because the registry website crashed frequently. Some were not given enough notice of interviews, or found they had been applied for a course they did not want.
Those trying to telephone found they were being on hold for up to an hour before being told to call back because there was no one available to talk to them.
Several said they would try to claim back their pound;12 registration fees in protest. One contributor complained that staff answering phones were unhelpful and lacked knowledge.
"The contact centre staff do not know what they are taking about," one said. "They need to be trained properly to deal with our queries. Our future careers depend on the GTTR system."
Another said: "I have an unconditional offer which I can't accept on the website. It just comes up with error messages. I'll have to ring them again.
"I now know the lady at the other end so well I almost sent her a Christmas card."
The registry processes almost 30,000 applications to post-graduate and professional graduate certificate in education courses every year on behalf of teacher training institutions, in England, Wales, and most of Scottish institutions.
However, a handful told the TES website they had experienced no difficulties.
One said: "My experience was good and pain free. Communications with the GTTR and university were good."
A registry spokesman acknowledged there had been some problems with its online system: "The GTTR values all customer feedback it receives and has systems in place to ensure that suggestions made are considered and channelled back into the appropriate areas of the service.
"Improvements to the online system are currently being developed, and, after consultation with our member institutions, will be implemented for the 2007 entry cycle.
"Applicants and referees are reminded that the GTTR website contains help text to assist them with the application process, especially on how to provide the reference via the online system."