Ok, I find myself caught with another issue: The Tongues spell states it grants the ability "to speak and understand the language of any intelligent creature, whether it is a racial tongue or a regional dialect." This does not specify granting the ability to read the languages, as Comprehend Languages does ("You can understand the spoken words of creatures or read otherwise incomprehensible written messages. ... The spell enables you to understand or read an unknown language, not speak or write it."), however in the Speak Language skill description it states "A literate character (anyone but a barbarian who has not spent skill points to become literate) can read and write any language she speaks. Each language has an alphabet, though sometimes several spoken languages share a single alphabet."
I am unsure whether this leaves someone affected by Tongues able to read and write languages the spell gives them they wouldn't normally know. I can see a case for either ("Tongues lets you understand languages you don't normally know, the Speak Languages skill you can read/write those languages if you are literate, Comprehend Lanuages only specifies the writing because it a: doesn't fully give the ability to understand a language (ie, you can't speak it) and b: gives the ability to read even to literate characters" or "Tongues doesn't specify that it gives you the ability to read/write the language, Comprehend Languages does specifically give you the ability to read them, therefore Tongues doesn't give the ability") , or even for being able to read/write only languages that share an alphabet with a language you know without the spell.
Your ruling on the issue for the game, Tawa?