If you lose avionics after some time, - you shut down APU incorectly. im not shure if this is bug or what, but deffinitely problem with manual :) manuals for 707 much more detailed.

Proper way to break generators in:

before APU start check GENERATORS BREAKER, TIE, FIELD switches in NEUTRAL position. They have 3 positions: open, neutral, close.
Same for APU BREAKER, FIELD switches

Start Battery, check battery ammeter shows negative so battery discharges.
Start APU as told in manual part III
APU BREAKER LAMP should light up.
switch APU BREAKER to CLOSED and back to neutral. BREAKER lamp should dim.
switch Essential power to APU, check battery ammeter show possitive current, so battery charges.
start engines.
GENERATORS TIE LAMP should light.
switch GEN TIE to CLOSED and Back to neutral.
GEN TIE LAMP should dim, and APU BREAKER LAMP should light.
set essential power to Generators.
shutdown APU.
check battery ammeter shows possitive current, so it charges from GEN.
check DC AC on all buses.
avionics should work on GEN power, not on battery.

this should be in manual, and it is there, but not so detailed :)

http://www.youtube.com/watch?v=528XovrLqFs - this video shows it. it's not mine and i got it from there.

there is another way to "fix" it.
go to SETTINGS\CONTROLS\KEYBOARD\ and map a key to GENERATORS\ALTERNATORS switch. no key mapped to this function by default. so after APU shutdown just click that key and all should work.

no *.CFG modification needed.

Also not covered by manual and not all may be aware of it.

****corrected THANKS TO member LOU****
how to feed engines 1,3 from central tank.
you should do all as in manual, so eng 1,3 crossfeeds closed, eng2 crossfeed open, all boost pumps on.
to feed engine 1 from central tank, just open eng 1 crossfeed valve,  and _TURN OFF_ boost pumps on Eng1.
Check that fuel quantity in ENG1 tank not decreasing. Eng 1 will use fuel from central tank.
If you leave boost pumps running on end1, it will eat its own fuel, and shut-down then the tank will empty regardless on crossfeed valve possition.

P.S. i got basic pack with 727-100 only. v 2.4. no problems with engine power, or whatever. I fixed sound problem as writen on this forum. im loading flight 2 times, and all works.