Zotero is grabbing journal titles from Pubmed from the JT field. This is fine for single word journal titles, but where the journal title has more than one word, the 2nd,3rd etc words in this field are not capitalized. For example Journal of biological chemistry. The reason is that this is the medline rule for compound names. Of course this is not right for citations.

I think Zotero should capitalize thus : Journal of Biological Chemistry

Also, Zotero may have to make allowances for the somewhat eccentric contents of this field for some journals. One clear example is for Journal of Neuroscience, where the JT field is:

Journal of neuroscience: the official journal of the society for neuroscience.

Just the first bit please!

excerpt from http://www.nlm.nih.gov/bsd/mms/medlineelements.html
Journal Title (JT)
This field contains the full journal title, taken from NLM's cataloging data following NLM rules for how to compile a serial name. The NLM journal title abbreviation is in the (TA) element.
Examples are:
JT - Molecular microbiology
JT - American journal of physiology. Cell physiology