Yeah I know, after being into digital audio for as long as I have, (anyone remember when a soundcard was the new thing to have?) I should have found a software package that I like more than the others, but honestly, I pretty much use whatever I have onhand. If I'm ripping a bootleg from mp3 to wav to burn onto cd, I usually use the extractor built into winamp. It's not very quick compared to others, but it works well. As far as burning it afterwards, I'll usually use either nero, or since I reinstalled my hdd, ezcd4. I know, that probably deserves a bitchslap, but it does what I want it to, and supports cd-text. With burning an audio cd I don't care what I use as long as it works. RIPPING an audio cd, however, I DO care. I use Audioactive production studio to encode my mp3s with the external Radium-modified Fraunhofer codec, at 192kbps NON-JOINT stereo. I rip wavs with audiograbber. I have a soundblaster live mp3+ soundcard. I'm telling you, it doesn't matter what you burn with as long as they were well ripped and encoded. Flange from Joint Stereo sucks.
As far as the two second cutoff thing, I dunno. Are you burning disc at once? If so, the problem may lie in the burning program you are using, but likely not..