I think that <PERSON> may well have complained to his Father but <PERSON> was too scared of <PERSON> to actually put in a formal complaint against him.
By the start of GoF <PERSON> has a reputation for being slightly (understatement) unstable. This is seen at the start of the book with on page 160 when <PERSON> says:
"<PERSON> you know Mad-Eye", said <PERSON> head, rolling it's eyes again. "Someone creeping into his yard at the dead of night? More likely there's a very shellshocked cat wandering around somewhere, covered in potato peelings. But if the Improper Use of Magic lot get their hands on Mad-Eye he's had it - think of his record - we've got to get him off on something in your department - what are exploding dustbins worth?"
"Might be a caution" said Mr <PERSON>, still writing very fast, his brow furrowed. 417
"Made-eye didn't use his wand? He didn't actually attack anyone?"
"I'll bet he leapt out of bed and started jinxing everything he could reach through the window" said Mr <PERSON>, "but they'll have a job proving it, there aren't any casualties."
and then later in the book on page 569 when <PERSON> says:
"D'you think it's too early to go and see Professor <PERSON>?" <PERSON> said, as they went down the spiral staircase.
"Yes" said <PERSON>. "He'd probably blast us through the door if we wake him at the crack of dawn"
Given this, it is probable that <PERSON> is scared that if he complains about <PERSON> then <PERSON> will hunt him down.
Another possibility is that transfiguration is not an altogether unusual punishment in the magical community despite it being not allowed at Hogwarts.
I say this because just afterwards, when <PERSON> is talking with <PERSON> she says:
"<PERSON>, we never use Transfiguration as a punishment!" said Professor <PERSON> weakly. "Surely Professor <PERSON> told you that?"
The fact that <PERSON> would have need to tell <PERSON> this suggests that there are places where transfiguration is used. Having said this, I don't believe that it being used in other places would have prevented <PERSON> from complaining. More likely to me is that he was scared of <PERSON>. 773