When you stack that many effects into a few tracks, you're run into buffer and mix issues that will cause noticeable pops. You would need a channel insert plugin, which is written for low overhead. Also, some mixes improve if you rearrange the order of the stack. Furthermore, some plugins have a learning mode, that is, it takes a few seconds (as the audio is sampled) before the effect is noticed in the edit. Gaps in the audio track will invoke pops, etc. as the plugin sees no data. So it maybe performing as it was written, (and not a fault of the host application). To know this for certain would be use a plugin from a different vendor and see how it samples the same area. There are plenty of free and good working VST's to be found. KVRaudio, BedroomProducersBlog and vst4free are a few places to check out. Adobe has an excellent plugin manager, so don't limit yourself to their offerings. Additionally, some plugins work better when placed into the master channel, which helps to reduce overhead and is better organized. You can also turn them off during your edits to speed things up, turning them back on before rendering.
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