Was this project begun in a prior version of Premiere Pro and then updated to the latest version?
A work around for your first problem is to place a clip of audio (with the gain dropped to -∞ db so that it is silent) in the gap that precedes the first real audio.
A work around for your second problem is to toggle the Solo and Mute buttons for the track a couple of times.
See if either of these suggestions help.
Both these issues occurred for me in a previous version but are not appearing in the very latest version of Premiere Pro. You might want to check and verify you are on the latest version.
These have all been new projects started on the latest version of PP CC. I just started a new project and put all my main talent audio on CH2 instead of CH1. I added a vocal enhancer in the track mixer to the track. An audio clip later in my sequence, with nothing before it started to make the chjit popping noise. I tried your suggestion of placing another audio clip with the gain dropped, right in front of it. It still made the glitch noise. I removed the vocal enhancer effect and it went away for now. Could it be the audio effect? I don't know. I also don't know how to get Adobe to respond.
I am producing several broadcast TV commercials per week, and it is becoming a real pain to deal with.