As others have noted, lowercase titles is a feature an not a bug, the idea being that the bibliography style is responsible for capitalizing or not title words according to the particular style it implements. However, there are obviously places where this is not what you want, as you have found: acronyms, proper names etc. in titles.
The general rule for solving this problem is to enclose the elements that must always be capitalized in {...}. However, as a rule of thumb, you should always enclose the smallest possible part. For example:
title = "A comparison of {P}ascal, {A}da, and {BASIC}"
title = "A biography of {E. M.} {F}orster"
not
title = "A comparison of {Pascal}, {Ada} and {BASIC}"
title = "A biography of {E. M.} {Forster}"
The reason for not surrounding the whole word in {...} is that the braces will also prevent hyphenation of that word. So it's best just to surround the smallest stretch of a word that needs to remain capiatalized. For proper names, this will generally be the first letter; for acronyms or chemical formulas it will be the whole thing.