Hi,
Thank you for your inquiry.

This highly depends on your setup and application.
To name the most common issues that can result in such a behavior:
1) The RTT buffer was created with the SEGGER_RTT_MODE_NO_BLOCK_SKIP flag.
=> Only the first couple of messages are written to the buffer until your buffer is full.
The other log messages are "thrown away", until the J-Link starts RTT and reads the data from the device.
=> The first messages are still available but the messages in between are missing.
2) The device uses low-power modes which make the RAM in-accessible via debug interface in this time.
3) No messages are send in this time.

To give a certain answer you would have to provide more information:
1) What device are you using?
2) Are you working on an evaluation board or on a custom board?
If evaluation board: Which one?
If custom: Does this issue also appear on an evaluation board?
3) How did you setup/configure RTT on target side?
4) How did you setup the J-Link RTT Viewer?
...

Best regards,
Fabian