1- not hearing anything from altera, i relaid out the board and solved this, sort of. there was only one jtag device. processor is netburner with only address, data and few control lines connected. there is a 75mhz clock coming from the proccessor, but not until it comes out of reset. there is all so a usb circuit that feeds a 60mhz clock ot the fpga, but not until the proccessor sets it up. some of the proccessor signals shared the same side as jtag. there is also a 25mhz clock.
what i did: rotated chip 90 degrees, so jtag is on the other side of proccessor's interface. changed from using snubber termination on data and no termination on other lines (remember, i have 2 other boards with exact same layout that worked just fine, the only difference is the components are 'closer' together); changed too, 47 ohm series resistor termination in 'every' line. also routed fpga 'done' signal to proccessor's reset circuitry and so proccessor is held in reset until the fpga is done loading.
i can now load a logic anaylizer and use it.
2- totally agree, "extremely odd", i was exteremely supprised when it was happening.
data coming in is latched at the pins, then this goes thru to the address register of the rom and the output is registered (-a- single clock). the worst case timing, as i remember, is 2.5ns, and the clock is 25Mhz. don't remember what the rom timing is, but sure it's better than 40ns.
power up the system and software guy's test software could say no problems. shut down and power up again and software guy may say, 'problems'. i also had a embeded logic anyalzer in the fpga to monitor input/output of the rom and other control signals. when problems were encountered, the logic anylzer all ways showed 'one' address, that was legal coming in, (same test software), and data out was wrong. power down and power back up and if it was failing (around 30% chance), it would be a 'different' address that was failing. now this was the decoding 10to10 bit rom, which 8 coulc be data and 2 contol bits. any illegal address would output a 0x3FF. when the rom failed, this was the output. i say this because, if the failure was during the bit loading of the fpga, i would expect a bit failure or some type, not the address failure it seems to show.
b- reset, power up of fpga. 'I' don't see anything wrong.
c- ? think it's as simpe as it could be (send it to if you want).
i stated, i took the rom's out and since then i've had not gotten any report back of continuous failures. my problem is that the boards are being used so i can't play with them. i have recently been able to get another board, with a cyclone3 on it, in the que for me to play with, but that might be another month out.
you've stated power problem for the stratix. could this be simular?
thanks
dave