Because $, is the character used when you give a list of values to the print statement, but you've used '.'s.
Ie. You're giving the print statement a single (concatenated) value, therefore the item separator is never used.
This might achieve your goal:
perl -lane '$,="\t"; print @F[0..4], "\t\t\t", @F[25..30]' file.txt
but "three blank columns" is a very nebulous concept.
Update: FTR, I might code that as: print join "\t", @F[0..4], ('')x3, @F[25..30];
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