hi David,
in my case i had to add this constrain in my top sdc file :
# **************************************************************
# Create Clock
# **************************************************************
create_clock -name {altera_reserved_tck} -period 30.303 [get_ports {altera_reserved_tck}]
the values might be different in your case even though i think these are the ones to be used.
the "altera_reserved_tck" is the one clock used to drive JTAG so constraining it can not harm your design.
In my case this seemed to stop the weird results i was having on SignalTap.
Tell me if you need more information.
Yannick