Доброго времени суток Господа знатоки!
Вот суть проблемы, у меня Цик2 с EPCS4.
Во время загрузки Цик2 из EPCS4 на пользовательских выводах висят "1" на время 2мс.
Как от этого избавиться?

Хелп читали? Вот, цитата из него:
Upon power-up, the Cyclone II device goes through a POR. During POR,
the device will reset, hold nSTATUS and CONF_DONE low, and tri-state all
user I/O pins. After POR, which typically lasts 100 ms, the Cyclone II
device releases nSTATUS and enters configuration mode when the
external 10-kΩ resistor pulls the nSTATUS pin high. Once the FPGA
successfully exits POR, all user I/O pins continue to be tri-stated.
Cyclone II devices have weak pull-up resistors on the user I/O pins
which are on before and during configuration.
The value of the weak pull-up resistors on the I/O pins that are on before
and during configuration are available in the DC Characteristics &
Timing Specifications chapter of the Cyclone II Device Handbook.

Ну вообще, перечитайте всю главу...