found not that

[color=red]1-We found, not that the reaction takes place at constant speed, but that it begins somewhat slowly and then becomes faster over time.

[color=indigo]2-We did not find that the reaction takes place at constant speed, but that it begins somewhat slowly and then becomes faster over time.

Is there a difference in the meanings of these sentences?
Does “1” imply that we expected to find that the two chemical substances react extremely rapidly?

There is not a great difference in meaning, but #1 may have a stronger suggestion of surprise at the result – as if it contradicts what was predicted or what someone else found. I think I would delete the first comma in #1.