You can clear the jump stack using the Empty stack menu command.
Each IDA Window has its own jump stack. This stack keeps the cursor locations. Many IDA commands use the jump stack, i.e. they save the old cursor position to the stack. For example, when you are at the address 3000:0100 and press the Ctrl-C key (find instruction), the 3000:0100 is saved into the jump stack and the search is started. Afterwards, you can return to the old position using Jump back command.
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