What is the application and did you notice similar behavior outside of it, e.g. being able to paste the currently selected text? I would also check your clipboard manager's configuration. Clipboards (usually) have a clipboard buffer (for CTRL + C -> CTRL + V) and a primary buffer (for selected text -> mouse middle button paste). Some problems arise from the confusing default settings of some clipboard managers, e.g. the synchronization of both buffers.
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