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Welcome to the world of VirtualDub timeline coordinates. It has everything of: mistakes, confusing design, unfinished work.
Basic rule of thumb is: everything you do in timeline control (insert, delete, move parts, select range) happens after filters. Curve points are in filters coordinates (or maybe even source?) hard to tell exactly because it does not work as explained in the documantation.
Also before I realized that timeline edits transform already filtered sequence I attempted to specify time positions in final (post-edit) coordinates and this made the situation even worse.
Good idea: never use both curves and timeline edits (except select range) in the same process. Also maybe don't combine any of that with time-scaling filters (deinterlace, interpolate, delete frames etc).
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