System works in debugger but not alone

How to troubleshoot following problem:

I have a system with an external RAM and Flash memory. I run very simple blinker software which scrolls LEDs on the board. Also, I hooked up two other LEDs to memory read/write signals to see if something is active on the memory bus.

I have configured cpu to boot from external flash and set the exception address in the ram. I have also configured IDE to place code and data into ram.

When I run Debugger from IDE - everything is fine: I can set breakpoints, step over the code, or even remove all breakpoints and just resume full speed.

When I program the flash with the same code and cycle power my software DOES NOT WORK. I see very short activity on my read/write LEDs but after a second ot two activity stops and the actual application never tooks off - LEDs do not flash.

I hooked up Quartus and loaded fpga via JTAG in order to signaltap it - the same happens. On the signal tap I see no activity on ram/flash after short time just after RESET - this confirms what I see: read/write LEDs do not flash.

Something is wrong, but since everything works in debugger I am not sure how to aproach the problem. Any ideas?