My system:
Ubuntu 10.04
Musescore 0.9.6 stable

The problem:
This occurs when the hide empty staves option is on. If the bar line is supposed to go through the staves (like a piano score,) and one of the staves that the bar line goes through is hidden, and at least two others are not, the bar line will break instead of go through.

To reproduce:
1) Create a new score for horn, trumpet, and trombone in that order.
2) Create two system breaks.
3) Double click the bar line and drag it down so that it goes through the whole system instead of breaking at every staff, which is default.
4) On the first system, add notes in the horn part only.
5) On the second system, add notes in the horn part and trumpet part.
6) On the third system, add notes on all three parts.
7) Go to Style >> Edit General Style >> Score, and tick the check box for hide empty staves.
8) Click Apply, then OK.

Expected result: on the second system, the bar line continues through in between the two parts.
Actuall result: the barline breaks and does not go through.

Attached is the result of the steps listed above.