One led is blinking too frequently using the hardware timer (stm32f103vdh6)
Just because it says it says 72MHz on the datasheet does not mean it will always run at 72MHz, it is the maximum it can run at. You don't show any initialization code so we can't tell if it has been correctly set to run at 72MHz. Inside the chip it uses much lower internal or external frequency source, which may be inaccurate.

But since you are using some kind of real-time OS, and using the delay function it provides, the delays are not exact. It just waits until the current millisecond count has been increased by the amount you requested. As the thing is completely asynchronous, assuming that you have 1ms system timer tick, there can be anything between 0 to 1ms before the next tick happens, so requesting 5ms will be in the range of 4-5 ms, so statistically speaking delay is always 0.5ms less.

I don't see why the led driven by TIMER2 counter even works. It will be awfully hard with a RTOS to hit to a point when counter is exactly 0 or exactly 1000. One count being 72MHz divided by the 7200 prescaler, so it's 0.1ms !