That's odd... Confirmed in my own 2012a.
It appears to be trimming all the entirely NaN rows from the end of your data.
I replaced line 348 with line 349, and confirmed the result is 347 rows long. Then I set the first element in line 360 to a non-nan value, and the result was 360 rows long.
I think this is stupid behaviour to have in a function, but nevermind.
Given that the files were created with save, you should do this instead:
data = load('file.txt', '-ASCII');
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