Show Opening Screen
When you start FSX and end it in a different way, the General Setting: "Show Opening Screen" is set to off. IF has a config.sys entry to always force this to on (or off) when you run or close IF (see initial screen help F1 at startup page).
Download Winds Aloft
When you start FSX with IF, the Setting: Display, Weather "Download Winds Aloft" is set to off. If you use a real world weather program, such as REX or ASE, this setting is handled. With FSX real world weather, you may want to check this box before setting off.
Proximity Alerts
When the Thermal & Ridge engine is running, a probe placed around the sim taking temperature and other readings may be interpreted as traffic by your tcas or proximity alerter. If you want to use the tcas during the flight turn off the Thermals.
Addon aircraft won't index
IF handles 99.999% of all known addon aircraft, but there may still be one or two that cause a problem. Make a new directory for these, say \NONIF, alongside your \Aircraft folder and place it in there. Add a line in fsx.cfg [Main] section (like the others) to show the path for FSX to find it. IF will now ignore it and can index the rest. Report the aircraft to me or maybe send in a copy of the aircraft.cfg.
Addon Scenery won't index
IF handles 99.999% of all known addon sceneries, but there may still be one or two that cause a problem. Use the scenery page in FSX to turn off the scenery (uncheck it), and run IF index again. Report the scenery to me and await an update to use the scenery with IF.
Another addon program does not start properly
Try the IF Cold & Dark setting "Pause", or uncheck both "Pause" and "Paused". Pause allows the sim to start running then pauses it, Paused starts the sim but does not allow any time to run.
Unable to build a route
Check the flight times and filters, are any of those airports within the set flight times allowed? Do the available airports have runways longer than that specified in the Aircraft Parameters? Try building a route in the map screen, search for an airport and with the buttons make it your departure and search again again for your destination.
Landings are harder to get right
The thermals can present you with sinking air just outside of a hot airport on a sunny day, the rising air over the airport. One exteme to another during final.