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RTX Task Switching - JTAG ULINK2

I am running into something really unexplainable at the moment.

I have been developing my project code and testing it with Keil uVision 4.03 and ULINK2.

When I run the code using the JTAG connector and uVision I can see it is working fine. However, when I disconnect the ULINK2 connector and power cycle the board I can see that something has change. I can notice it right away because my GUI taak (low priority) runs slower. It also looks like it is doing this by a factor of 3.8.

What could be causing this?
Could it be that ULINK2 changes the RTX configuration?

I double checked SysTick timer and oscillators and their configuration is the same with and without the ULINK2.

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