I had this problem, as well as a "temperature dependant" low side pressure
switch (officially called a pressostat).  It's the unit mounted high up in
the middle of the engine bay just as the a/c pipes go into the firewall.
Just above the exhaust manifold.  The a/c would work fine when the car
started off, but if stopped for say 5 minutes, the switch heated up due to
engine bay heat, and the system would no longer cool. The refrigerant would
normally keep the switch cold as long as it was running.  This was rather
tricky to find, but as there is a valve under it, it can be replaced without
losing refrigerant.

A week following its replacement the compressor "protection" switch started
playing up, with your same symptoms.  As Mike suggested, bypass it.  Apart
from being a bit tight to get your fingers into (let the engine cool down
first) it's a plug and socket job, you don't need tools. Although different
connectors are used, they will interchange.

Both these problems came straight after the evaporator had been replaced due
to a definite refrigerant leak.  I can't see how these three events could
possibly be related, but I know I would have spent a fortune if I had to pay
a dealer to chase them.  In fairness, it would probably have cost them lots
to chase an intermittent fault too.

I bypassed the protection switch at the beginning of last summer (December
2006) and have had no problems since.

If you're interested in exactly how the system operates there is an
excellent description here
http://au.geocities.com/ozbrick850/aircon-keithP.html

Regards
Barry