It's been a while and I've already finished that project but my problem seemed to have been related with the video formats. I was like adding the non-encoded video straight from AE at first but when I tried encoding it as mp4 or avi using Handbrake and then adding it inside Blender, there were no frame droppings at all. I have an old 6 threaded AMD FX 6300 btw. And thank you guys for the feedback. ^^

I think i finally debug this. The issue was due to the clip resolutions. If the clip is 1080p you'll get stuttering and most likely will stuck with low fps count but when you use 720p (basically any resolution lower than 1920x1080) you get more than 29 fps but again you can't go beyond 46 fps this time. (I believe this may change depending on your CPU threads) So i'm guessing the more resolution you have the more processing power it takes and as a result you get a low frame rate. I still think this shouldn't be the case and blender should be able to run smoothly at 1080p as well. My problem is kind of solved here because I'll be comfortable to work with 720p+29fps. That's enough for my scenery but I think someone should look over to this subject since blender is planning to go more pro with the upcoming updates, optimizing this would be a major ease when it comes to match moving btw. thank you for your interest @matc (matc) :)

In T68181#744326, @matc (matc) wrote:

Appears to be working for me. Are you stuck on 15 fps even on the default scene, when you add the background clip?

Exactly, even with a fresh startup when I add a clip it doesn't live up to the fps that I've set in the output settings. I tried using the playback options
such as av sync and frame dropping but it was the same. In addition to that I thought the problem could be related to my preferences and restored them to their factory settings but still no luck :(