timer3 interrupt jitter

[ErsaFap]

Using arduino 1.6.1. Board - mega2560 R3.
I have some empty project. I try to run 10 us timer interrupts and it is very unstable. It is something disables interrupts for too long. I have empty loop and setup. I am using timer3 compare mode. This affects the timer interrupts. How can I fix this?
Im sorry for my rough English.

[sandeepmistry]

Hi @ErsaFap,

Could you please provide a sketch that can be used to reproduce this?