Adding a passive adapter into the mix should not change how things currently work. It's a little difficult to get at what you mean. DVI to DP adapters are rare-they almost always work the other way around. Most video cards are limited to two dvi/hdmi/vga signals but are not limited with respect to the number of displayport outputs. There are, of course, variations on what is supported.
It sounds to me like you have two screens connected to the dvi/hdmi outputs and mini dp to dp passive connected to a dp to dvi active adapter. If that is the case, your three screens should work.