The reason is that "ce" does not express a grammatical gender, whereas "voiture" is feminine. "ce" is a demonstrative pronoun for things to which a gender is not defined, that is saying for things that are neither masculine nor feminine, as in French those two are the only genders nouns can have. When you have a sentence such as the following there is only one gender the antecedent can have.

• — Il m’a dit qu’il allait à la plage demain.
  — Ce n’est pas vrai, il ne te dit pas la vérité!

The antecedent of "ce" is "il va à la plage demain"; you can call that what you want, an assertion (une assertion), a fact (un fait), even an answer (une réponse); therefore it is considered as having no gender although we don’t bother much with that in grammar.

If you want a demonstrative pronoun for "voiture" you must use a feminine one, that is either "celle-là" or "celle-ci".

With “être + adjective” (or a noun that adopt an adjectival syntax for this particular construction, like with occupations), il(s)/elle(s) is used when the subject is 1. a Noun phrase or an independent pronoun and 2. specific.

In all other cases, ce is used: infinitive (se réveiller, c’est dur), subordinate clauses (que tu te soies réveillé, c’est bien), quantified NP (Quatre repas par jour, c’est beaucoup), partitive NP (des chips, c’est pas nourrissant) generic definite NP (l’hiver, c’est fatigant – that is, winter in general, rather than the particular winter we’re in) and so on.

It has nothing at all to do with gender.

In the case of sentence in the question, we could rephrase it as “J’ai une autre voiture, mais cette autre voiture est bleue”. Since “cette autre voiture” is both a noun phrase and specific, we have to use one of the +specific +NP pronoun, with the right number and gender agreement, that is to say, elle.