Hi,
Thought I would post this as I could not find any info if the cheap programmer had problems with SignalTap or not. Hopefully it will be useful for others.
Been using my cheap clone ("Rev C" £3 GBP or so from ebay) to program Altera FPGAs for a while without problems.
Tried to use it to with the Altera SignalTap logic analyser recently, and got "Invalid JTAG Configuration".
Was not sure if it was the cheap programmer that was the problem, or something else.
This was work work so I splashed out and got a genuine Altera USBBlaster II (Mouser was the cheapest, but still expensive!)
The problem no longer occurs, so it looks like the problem was the cheapo programmer after all.