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You said you're exporting as an mpeg2, are you separating your video and audio (exporting a separate wav file), or are they combined? What are your audio compression settings?
The way I use the multiband compressor effect is by means to apply a digital simulation equivalent to a mixer's compressor in analog sound processing, I do not know if the 'compression' of digital data actually happened.
But I'll try to show what settings I made in the Multiband compressor sound effect:
low freq attack time: 0.10 millisecs
low freq release time: 144 millisecs
Compressor Ratio: 2.5
mid freq attack time: 0.10 millisecs
mid freq release time: 145 millisecs
Compressor Ratio: 2.5
High freq attack time: 0.10 millisecs
High freq release time: 144 millisecs
Compressor Ratio: 2.45
Some details of my video format: The video and sound are captured in combined format via firewire from HDV source, edited and exported as mpeg2 720x576 combined video and audio (no separation). The timeline sound is noise free, only the exported video contains the noise, pops, squeaks, etc.
I have exported the video and audio together in Adobe Media Encoder, settings as follow, video I created VBR 2 pass, 5 for quality, 25 fps progressive, level/profile main, bitrate as follows: 2 min 4 Target 6 max, for sound settings: format mpeg, layer II, stereo, 16 bit 48 kHz, bitrate 224 kbps
I think I found the solution. Here's the trick I realize after numerous experimenting. It is concluded that not to nest a sequence, say sequence A, where you already applied sound effect, into another sequence, name it sequence B. If you use sequence B (containing sequence A in it) to export video, you'll get unclean sound whereever the portion you've applied the effect. So just export directly from the sequence you have the original footage or video footage, try not to export from a sequence that contains a sequence /sequences, if sound effects are applied.
I can confirm that I have found the same (very annoying) problem. Nesting a sequence containing audio compression into another sequence produces very poor quality audio (sounds like over-driving/clipping to me) in exported output (playing the second sequence in Premiere sounds OK).