Having trouble aligning downbeats with tempo

[pianosdr]

Hi there,

I'm running into a problem getting my music to align with the bars/beats in Pro Tools.

I'd like to know how to get my music to align properly with the bars being generated after I've played the music on my controller. Even after identifying the beat of my music, and then setting the session tempo to that beat, it appears that the score editor is still not aligning the beats with the bars properly.

As a simple example, I have a loop of 4 notes played on a bass, and I looped that riff over 2 bars. One note is supposed to be for each beat of the bar. And although I've now already identified the beat that I played and quantized the notes to that rhythm so that my timing imperfections while playing have been corrected in the software, Pro Tools still isn't aligning the bars properly. Bar 1 is playing all 4 notes of the loop, and then also tacking on a dotted 8th note at the end of the bar which is tied to a 16th note of bar 2, when in reality this entire note was supposed to be the 1st beat of bar 2. This error then obviously continues throughout the rest of the loop, gradually causing the downbeats to get farther and farther away from each successive measure.

How can I get Pro Tools to properly recognize where each bar is supposed to land in relation to my notes? I've googled everything I can think of and just can't figure it out.

Thanks!

[pianosdr]

Here's an image to help illustrate what I'm talking about in the simple example music. The bars are supposed to align with the notes shown in the image, but even after tempo identification and quantization, the bars are still remaining off.

[pianosdr]

I'm also running into an issue with quantization where quantizing is turning all of the notes I quantized into simple blips, where it barely sounds as if they're being played at all. This seems like a bug, and I have seen a few posts mentioning this in the past in google searches, but no solutions to that either.