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Everything works fine without reboot

Hello all.

We're using the MCB1760 Board and try to communicate via Ethernet with a PC with a RealTime Linux. The Ethernet communication on the board is interrupt triggered.
If we program the device via USB JTAg and let it run everything works fine. The MicroController gets every Message from the PC via Ethernet. The connected and controlled servos are set just in that way we liked it.
But after a reboot of the MCB1760 Board we can notice strange behavior. Ethernet Messages seem to take a lot longer to be set by the MCB Board(about 50s).
Unfurtunately this behavior can´t be observed when using the debugging function of uVision4. Because the controller is programmed again before a debug session starts.
This behavior leads to this questions:
What does the board after a reboot do which compromised our code or the behavior of the board?
Which are the differents between just programming the board and programming and do a reboot?
Is this issue caused by the bootloader?
How we can fix it?

Thanks for any advice.