I noticed that after a server restart the Steel i get from smelting steel dust changes from time to time. Sometimes the result is mekanism steel sometimes the result is TCon steel. normally that is not a problems but it leads to problems while auutocrafting since only one kind of steel is expected.

I am using the modpack Resonant rise 3.4.0.2 it is currently running 9.0.1 (1.7.10) but since the bug persisted from mekanism 8 onwards i will report it anyway. (and because i did not see anything in the changelog concerning this issue.)
There are no errors in the Log.
The steel has been smelted using the Smelting factory.

Okay thanks. also if the steel turned into railcraft steel today? (maybe my server just feels fancy ^^)

This isn't mine or TC's fault. Use Mekanism's Oredictionificator to sort out issues like this.