$$$\left(\begin{array}{lcr}a_{\tiny1}+d & a_{\tiny2}+d & a_{\tiny3}+d \cr b_{\tiny1}& b_{\tiny2}& b_{\tiny3} \cr c_{\tiny1} & c_{\tiny2} & c_{\tiny3} \end{array}\right)$$$
renders
which I imagine should solve your problem. But that syntax won't be "portable" to standard/canonical LaTeX notation. For that you'll need the \\'s, and I'll leave you to take up the bug-or-feature question with Martin.
It still looks like you're having some kind of & vs. & issue. Mimetex also recognizes & as an "alias" for & in _all_ contexts. So you can separate array columns by writing
a & b & c
That will work _regardless_ of whether or not the "front-end interpreter" translates & to &. Of course, as before, it's not portable syntax. So you can use it to get around html-induced problems, but you're kind of locking yourself into mimetex.
Mimetex has several non-portable syntax extensions to accommodate occasional html incompatibilities that have been brought to my attention by users. You've tripped over the two most common ones. But the usual & problem is that some html-friendly editor sees you type & (intended for LaTeX) and automatically translates it to & (incorrectly assuming it's intended for html). You seem to be having some other variation on this theme, which isn't exactly clear to me. But I'm guessing that typing & wherever you want & will clear it up.