The Doctor attempted to convince himself that fixed points were just a theory and that he could change them, however, The Waters of Mars proved the opposite - that he is still limited at fixed points, and further that his megalomania, when not tempered by a companion, would lead to more tragedy rather than less. The lesson of Mars was not that he could change fixed points; it was that fixed points would survive his attempts to change them.
This is consistent across the two episodes you mention:
In the case of Father's Day, the time cleaners came because the pivotal point - Rose's father - needed to be cleaned up.
In the case of The Waters of Mars, the time cleaners do not need to come, because the pivotal point - Adelaide Brook - cleaned herself up. Her living was the pivotal point; in committing suicide, she resolved the two timelines. Her tragic death following the destruction of Bowie Base One remains to inspire her granddaughter - all that changed was the location of that death.
Had she not committed suicide, it's reasonable to assume the time cleaners would have shown up eventually. They didn't appear right away for Rose's father, either.
A bit more about the Doctor's mental state in Waters of Mars...
To quote the Tardis Wikia:
Mostly a character piece, it showed the extremes to which the Doctor
would go when unregulated by either other Time Lords or companions.
The Transcript shows the point at which the Doctor contradicts his earlier statements about the fixed point being immutable. This is the speech I was referring to when I used the term "megalomania" earlier:
But you said we die! For the future, for the human race.
Yes, because there are laws. There are Laws of Time. Once upon
a time there were people in charge of those laws, but they died.
They all died. Do you know who that leaves? Me! It's taken me
all these years to realise the Laws of Time are mine and they
will obey me!
and the Wikia again describing the climax of the episode:
The Doctor argues that the rules of the Time Lords were only valid
while their civilisation existed, and that since he is the last of his
race he has total authority over time. He states that he no longer
considers himself to have survived the Time War, but to have won it
and proudly declares himself the "Time Lord Victorious" and remarks
that with this power he will now be able to save influential figures
such as Adelaide as well as "little people": the likes of Yuri and
Mia. Horrified by the Doctor's newfound arrogance, Adelaide says: "Who
decides how important they are!? I don't care who you are, the Time
Lord Victorious is wrong!".
The transcript again:
[Adelaide commits suicide. The Doctor remembers her saying:]
I don't care who you are. A Time Lord Victorious is wrong.
The DOCTOR turns and looks in the opposite direction.
I've gone too far.
And recall that this is all happening after the Doctor had been warned that his death was approaching. The next few lines of the transcript:
[OOD-SIGMA is standing in the road. The DOCTOR falls to his knees.]
(to OOD-SIGMA) Is this it? My death? Is it time?
[OOD-SIGMA vanishes. The DOCTOR stands and enters the TARDIS,
slamming the door shut.]
The Doctor was pretty mentally unhinged at this point. Unregulated by a companion, running from his foretold death, his arrogance reached new levels and was sharply reined in when the fixed point re-asserted itself with Adelaide's death.
So - to wrap this back to the question - the doctor didn't say it was his theory, he said it was a theory:
This moment, this precise moment in time, it's like... I mean,
it's only a theory. What do I know? But I think certain moments
in time are fixed.
It's one of the theories that the Time Lords ruled in accordance with. And the Time Cleaners are phenomena that act in a way that supports that theory - probably not the only support, but one of them. In Mars, the Doctor convinced himself that he could rewrite rules; he was wrong, and Adelaide proved it before the Time Cleaners were needed to reconcile time.