Not real sure what you're talking about.
Could you post a screenshot of your issue.
Also you should mention what vesion of the game you're using as well.
I am familiar with an anomaly that occurs in your military timeline graph. Basically it occurs in some versions and revisions of the game and is due to a "wrap" that occurs at a military rating of about 6 million and again at 12 million.
To see this you have to achieve huge levels of military strength, generally you need 6+ fully populated military resource mines along with 17,000+ ships along with all of these ships being under a military starbase array consisting of 24 SB's. Even then it's tough to achieve these levels but it is possible.
Here is a screenshot of what I'm talking about.

Note the "wrap" occurs at a point in the game where I upgraded 17,000 huge hull ships with 1 attack and 1 defense point into ships with 25 attack points and 550 defense points (prior to all bonuses of course). This appears as a decline of my military strength from a value of about 5 million to a value of about 3 million because the display "wraps" twice, once at 6 million and again at 12 million.
However the display at the bottom of the main screen shows the "true" shape of the curve.

The above screenshot shows the main screen military strength graph along with my 24 military starbase array.
Note that the AI's military strength is invisible at this scale merely because of the huge value of my military.
One other point to note is that your military strength is shown under your Civ Manager Stats & Graphs tab as in the following screenshot. The thing is that the value under the Stats & Graphs tab displays your current "real time" military strength whereas the Military Timeline in the Civ Manager is delayed by one turn and the main screen military graph is delayed by two turns.

Also note that the above shows the bar graph section which lists the opponents in this game as "no contacts". This is because these screenshots are from the endgamesave file where I have eliminated all the AI's and will win in the following turn. In reality this game was against 9 AI's in a gigantic galaxy in DL v1.4x.
So does this have any correspondence to what you're talking about?