I have had similar experiences. One explanation might be that the AIs are doing a lot of tech trading amongst themselves. I do not think they do that, but it would explain matters. That is, one trades beam weapon advances for, say, moral techs while still another trades government advances. One solution is to emulate that sort of behavior, as I'll discuss further below.
The standard posting on this Board is that the AI gets no extra bonuses until the level above "Tough".
One thing you might do is to see if you have techs that the screen shows the AIs do not. If there are items you can trade that you have researched, then part of the answer might be that you chose different things to research. Another thing is to watch the AI treasuries. You can see them by going through the motions of a trade without ever "sending". If their treasuries suddenly drop quickly, they may be rush buying more than you are (like research buildings).
Another possibility is that the AIs simply have a more efficient research sequence than you are doing. That is, the AIs may concentrate on researching higher research facilities earlier or, perhaps, they do NOT research those higher facilities while you are the one doing that.
In my games before I moved up in difficulty and had to change tactics, I often fell behind in research early, only to run past the AIs when I got my planet count up and had a higher base. In my more recent games, I tend to get ahead early when I run around the basic techs, then fall increasingly behind as the AI bonuses kick in and I shift to production improvements and colony rush. (At higher difficulty levels with lots of AIs, if you are at all slow to colonize, you end up with very few planets - I try to grab at least 15 - 20 on the largest maps) Eventually, I tap the minor AIs and trade with Diplo bonuses to get what I need, and go on from there.
One help is that, instead of researching all the techs up a line, trade to jump in several techs from the beginning of that line. Thus, maybe you should never use research resources to research Beam Theory, laser 1, laser 2, and laser 3. Instead, research something else you need, then trade it to a Minor for Laser 3, and research from there.
