The book "Startupland" that chronicles Zendesk talked about this exact problem. One of the 3 founders had "family" to take care of and because of that, he wanted a higher salary. The 2 other founders were thinking, "what?!?
you're not the only one making sacrifices here!"
After some discussion, the 2 other eventually agreed to it but they really resented it and it was a source of bad tension for a long time.
Zendesk eventually got to the IPO so the 3 got past that unequal salary episode but the soap opera drama doesn't seem to be something you want for a struggling company.
(Side note: I think it's unfair to downvote jacquesm for bringing this up. Even if you disagree with his opinion, it's still worth leaving the text ungreyed to discuss pros & cons.)
 coincidentally, Zendesk is one of the companies in Point Nine's portfolio:
(However, author Christoph Janz joined Point Nine in 2011 and Zendesk started 2007 so he may be unaware of their early salary drama.)
FYI, Zendesk was a "pre Point Nine" angel investment from me that I made in 2008, but I wasn't aware of these discussions among the founders. Maybe they took place before I joined or they wanted to keep them to themselves.
Well sure, I agree it doesn't have to. But as this thread has shown, it's a contentious issue demonstrated by:
(1) furious downvoting & upvoting of jacquesm parent comment,
(2) many comments in this thread from opposing sides debating it
(3) chapter from Zendesk founders' book discussing the uncomfortable tensions it caused
Therefore, saying "paying one founder more than another can cause conflict. But it doesn't have to." -- sounds somewhat naive. To be clear, I'm not saying _you_ are naive. It's that your sentence sounds like it brushes the human complexity under the rug. (We can also say "paying everyone equally also can cause conflict, but it doesn't have to." -- a kind of tautology that's true but doesn't really inform us.)
Also, it's important to stress the timeline of the startup:
It's one thing for the startup to not exist yet and the 3 founders are just sitting around a dining table and agree that 1 founder should get more salary because he has kids.
It's a very different situation when the startup is already up & running for a year and the 3 equally paid founders are living on cheap ramen to keep expenses low and make the struggling company survive. If at that point in the timeline, if one founder asks for more salary because his wife is pregnant, don't be surprised if the 2 other founders will react very negatively. It's human nature.
Recruiting a parent with existing kids to create a new startup is a different dynamic than increasing a partner's salary because they have a family after they've been working. The other founders may feel like they contributed the unspoken sacrifice of not having kids so subsidizing another person's family at a critical time can seem unfair.
One can "agree" to something because of business expediency but simultaneously have a human response that it feels unfair.
As analogy, I'm sure many programmers have "agreed" to a low $55k salary and took the job but simultaneously felt that the company was unfairly compensating them because they thought they were worth $100k. Unfortunately, agreement doesn't override human feelings.
If you were interpreting my blurb from the book that the 2 founders were constantly throwing the unequal salary in the 3rd founder's face, I don't think that's what happened. The book made it seem like it was a more like a silent resentment. Also, the salary argument came up after Zendesk was already established and running. I didn't previously make it clear that this wasn't 3 founders deciding on unequal salaries when Zendesk was just an idea on a napkin. If one agrees at the founding, that should remove triggers for resentment.