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?
Keep in mind, this is *not* a support forum.
Our engineers will try to answer your questions between their projects if possible but this can be delayed by longer periods of time.
Should you be entitled to support you can contact us via our support system: segger.com/ticket/ Or you can contact us via e-mail.