IORD_ALTERA_AVALON_PIO_DATA to slow?

I use Nichestack, too. It uses two high priority interrupts to manage ethernet rx and protocol: this is leading to the delay you are experiencing.

Nichestack also includes some critical pieces of code where isr are temporarily disabled, so you can't attain such a precise timing as you require, even if your sampling is made through a highest priority timer interrupt.

the only way to perform precise sampling at f>100kHz is to make it with hardware, dma or similar.