In the Properties of the beam under Construction; set the Start or End Offset (Depending on what end of the beam is touching the other end; ie. Start to Start or Start to End) to be the distance you want the beams to be apart. Initially have the "Drag Structural Framing Component " dot to be the same as the other beam. This will join the two beams. Then set your offset and the beams will still be "joined" if you were to right click and select "Select Joined Elements" but graphically it shows them separate. Even with bar joists, the bottom cords do not graphically stay joined.
I've had this same problem many times - and I finally figured out a fix. I know this is an old thread, but hopefully this can help someone else.
I was modeling an angle mounted to the bottom of an existing precast beam, bracing the top of a column. See below -
However, when i placed the ends of the beam where I wanted them, the beam automatically joined to the precast and most of it disappeared. When it did this the option for start extension grayed out. I also did not get any options to disallow join in any view (I don't think that option exists for beams, though I'd love to be proven wrong there)
Solution - I placed the ends of my brace beam where they were not touching the adjacent beam. Then I adjusted the start extension to go under the precast. Works perfectly, and stops trying to fix itself away from where I want it.
Hopefully they'll give us a universal disallow join option that always shows up - until then, this could fix most of the issues I run into with beams.