The "power requirements for cyclone iv devices (https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/cyclone-iv/cyiv-51011.pdf)" chapter of the handbook discusses the rail sequencing, amongst other things you need to consider. In short there are no sequence constraints:
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You can power up or power down the VCCINT, VCCA, and VCCIO pins in any sequence. The VCCINT, VCCA, and VCCIO must have a monotonic rise to their steady state levels. All VCCA pins must be powered to 2.5V (even when PLLs are not used), and must be powered up and powered down at the same time.
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The power supply design may well be proven but the performance of it may well vary from design to design. Different loading and layout will see to that. Nothing you describe is wrong. However, how good are the supplies at the FPGA pins? Have you looked at them with an oscilloscope? What they look like there is what matters. Plenty of local decoupling capacitors can be very important.
I don't think your choice of voltage regulator is appropriate. 250mA for VCCINT for an FPGA that size just doesn't sound like enough to me. Have you planned this with the "
powerplay early power estimators (
https://www.altera.com/support/support-resources/operation-and-testing/power/pow-powerplay.html)"? What current are you expecting VCCINT to draw? I suspect the planning spreadsheets will estimate it's more than 250mA. Are those regulators getting hot? Is it one of those that's failed (as opposed to the FPGA)?
The 'random logic generator' doesn't concern me. Random transitions are perfectly acceptable providing the signal they are generating conforms to the I/O standard specifications for the FPGA. Any over/under-shoot is what might shorten the life of the device. How that manifests itself might be as simple as the particular I/O pin failing. However, it may well be something else.
You also ask if the USB-Blaster draws current from your board - yes, but not a lot. Refer to the "
usb-blaster ii download cable user guide (
https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/ug/ug_usb_blstr_ii_cable.pdf)". Does it drag your 2.5V rail down when connected/operating? That would be a bad sign.
A single 2.5V linear - like you have - should be enough. Does it get warm? How much current is it delivering? Whether you are simply programming via JTAG or debugging will not significantly affect the current the USB-Blaster is consuming.
I think you need to focus on the regulator for VCCINT. It just doesn't look to be up to the job.
Cheers,
Alex