At which stage of the configuration process will the I/Os drive with the configured drive strength and slew rate?
Spartan-3E devices will configure the I/Os at the very end of the start-up sequence. By the time GTS is released, the I/Os will still be driving the default I/O standard. The new I/O Standard will be applied after the entire startup sequence has completed.
If a lower drive strength is being used and the I/O is set to drive a 1 initially, the device will drive the I/O at the increased drive strength for a couple of clock cycles.
To resolve this issue, the I/O can initially drive a 0 as opposed to a 1.