Why Am I Getting These Weird Rhythms‽
I hate to be the bearer of bad news, but most frustrations that notation users have with these programs is the concept of using a MIDI controller/keyboard with it. Most feel that by plugging in the controller, they can press record and their notes and rhythms will magically appear in perfect form on the screen. Here is the bad news: it rarely ever works that way.
There is an evil-doer for this problem: LATENCY!
Latency is the amount of time it takes for your computer to recognize you are playing a note and plays it through the speakers. If your computer is not up to speed RAM- and processor-wise, you will experience a very high amount of latency.
Other things that affect this: running multiple programs in the background, even using too long of a USB cable, running your controller through too many other peripheral devices, or even Virtual Instruments can throw it all out of whack.
How does this affect your score, you say? If you are listening to what the computer is notating against your playing, it will really throw you off. Even if it's behind by 1 second, you have to constantly adjust your playing.
However, there is help for you if this is your problem!
For SIBELIUS:
There is a device that really hinders your ability to use Flexi-time correctly: Microsoft GS Wavetable Synth. This is a default playback device for Sibelius 5 and can be the default in Sibelius 6 if the supplied Sibelius Sounds Essentials sample library. In order to get this fixed, you should choose Play -> Playback Devices and choose Sibelius Sounds from the Configuration Menu (Sibelius Essentials 32 sounds in Sibelius 5). This will activate the best player for you to use Flexi-time. 
If you are stilling having problems, go back to the menu above and click Audio Engine Options (bottom right of the menu). Choose the best available choice into the Interface menu (should be an ASIO interface…if none is there, look into getting an ASIO-compatible soundcard or audio interface, or try installing the ASIO4ALL universal ASIO audio driver). Set the Buffer size to 1024 samples or lower to reduce latency even more. The goal is to have latency to less than 50ms (this should give you optimal results).
After all of this is set and done, you can help avoid all of those funky rhythms by doing this: Go to Notes -> Flexi-time Options (or hit Ctrl-Shift + O for Windows; Shift-Cmnd + O for Mac). Under Flexibility of tempo, select None (non rubato) and under Voices, make sure there is not a checkmark in Record into multiple voices and have 1 selected. Go to the tab "Notation," and adjust the minimum rhythms to what you believe the lowest note value will be in your playing (this will help with getting rid of those nasty 32nd and 64th notes that come up). Finally, if you want to stop those triplets from happening, adjust the tuplets section.

Sounds like a lot of steps, but in the long run, this will help tremendously since you won't have to consistently fix your score.
I'll have the fix for Finale next week (oooo, suspense!)

