MAX10 .pof file issue, quartus II and usb blaster
I hope you solved your trouble at this time.

From what I learned from MAX10:
JTAGEN has no influence on programming, on all my board it is now pulled down (I use 10k), this prevent entering JTAG when I/O sharing is selected, no influence if JTAG sharing inactive.

NConfig, Nstatus, Config_Done need a pullup, never use these pin as input, low on power up never enter user mode, this was a fault on my first board, after first programming never get again programmed. Chip in this state got warm. After rework again got programmed first time then again same sequence. After a long inspection, I found nConfig was low at boot time (it was connected to an IRQ). Removed this threat board restarted working. 

Leave a pad or jumper to help you get NConfig, Config_Done low at startup to avoid enter user mode if you experience trouble to reprogram.

Pull down TCK thru 1K, pull up TDI, TMS (10K) TDO is not sensitive.
Noise on TCK and TMS can activate JTAG state machine with unknown behaviour.

On some commercial demo board I seen this network on nConfig, it do dual purpose, delay entering user mode, provide free pull down from MAX10 driver.


                    /---|==R==|---- NConfig
            R       |     C
VDD------|=====|----+----| |----GND


At last power ramp if too slow enter a critical state prevent programming .pof, from your word this isn't your case.