Calculate Consensus


I'm mostly using Jalview to view alignments.

Normally, when I open one of my alignment files (.afa or .jar), I get
a consensus sequence at the bottom and the alignment is automatically
coloured by conservation.

But weirdly, sometimes when I open the same files, I don't get any
consensus sequence (and hence no coloration).
Can anyone tell me why? I'm not changing the settings!

Sometimes, restarting the program will solve the problem (until it
appears again a few files later). But not always. I have also found no
pattern as to after how many files this happens (I usually close files
before opening the next, so it shouldn't be a memory problem, right?).

Any idea what's happening and what I can do to prevent it?

The settings I think are relevant for this:
Preferences => Visual (Open New Alignment)
I have ticks in
- Show Annotations
- Quality
- Conservation
- Consensus
- Show group: consensus
- Consensus: Histogram

I'd be really grateful for any advise.
Thank you!