When it happens again we will try the suggestions. Because it happens on different types of multi-engined A/C it must be an inherent fault in FS9. If it is something common to all aircraft could it be in the FS9.cfg? For me to try and figure that out is the same as a pig looking at the insides of a watch only the pig would be smarter.

Most often this problem is the symptom of a misbehaving gauge
sending continuous "KEY" events. These events tend to interrupt
and multi-key user input such as "E" + "1" + "2" etc....
As a result, FS9 only see's the "E" and defaults to engine 1 only
control.
A fix for this problem has be around for a few months but I
forgetthe name of the gauge that accomplishes this. I believe
it is a Doug Dowson creation.
I generally just dive into the panel.cfg and find the offending
gauge, notify the provider of the package, and then either
fix or replace that gauge....but that's just me, the retired engineer

Paul