I keep seeing this text '~C 1, 64' or something similar above a stave, what does it mean?
It is a MIDI instruction for Sibelius. This document covers MIDI directives:
I believe this particular message is a pan center command for playback.
We don't need a picture, the description is sufficient. It's a MIDI controller message. CC1 is Modulation. Now, I'm smelling a rat here. The default position of the Modulation Wheel (or equivalent) on an input device would be 0. 64 is a perfectly possible value, but consistent 'Cx,64' messages suggest a controller whose default position is 'centre' rather than 'off', like CC10 (Pan). Or one that has only two values - CC64 (sustain pedal) normally only takes values 0 or 64. But let's not read too much precision into your "'~C 1, 64' or something similar".
You can tell Sibelius whether to record CC messages when inputting using Flexitime. But if the MIDI file was imported from an outside source, it's common for it to start off with a whole bunch of MIDI commands, designed to initialize a General MIDI device for playback.
With a newly-imported General MIDI file, it's likely the CC messages are the ONLY items of Technique Text, so you can get rid of them all with a simple Filter operation for that Text Style. No need to filter specifically for text beginning with '~C' as is often advised.