So this is normal, my counter is not faulty? But why sometimes normally update the frequency from 10Mhz to 1kHz, and sometimes not? Is this something buggy in the firmware of the counter?
Yes, I believe this is perfectly normal.
The reason sometime it happens and other times it doesn't, it probably has to do with when in the change happens. If it's towards the end, or closer to some sort of checkpoint, you probably won't notice it. Also, it depends on what frequency you switch to, or if you go through other frequencies in between. For example, if you switched to 100 kHz, then it would get stuck only a little.
Edit: I just tried it with the settings you mentioned and I have a tough time doing it at 0.1 s gate time, but at 1 s, it's always doing it.
Edit 2:I verified this behaviour on a newer unit, and it behaves exactly the same.
Keep in mind, that based on your luck, it could be waiting up to 10 000 longer than the set gate time, when you switch from 10 MHz to 1 kHz.