As pseudoswede said, the projected (at the end of month) profit (or loss) in the regular finances page will probably be of much better use. Use the Operations Dept report only to get a better understanding of where your money is coming and going to.
But no, it's not a very good thing if your retained earnings keep consistently going down. Keyword here being "consistently." When you rent a gate or pay market research to create/edit a route, it's natural for your airline value to go slightly down. As long as that expense allows you to earn more money in the future, it's quite alright.
So, as you suspect, switching gates may explain part of your value loss.
Also, be aware that monthly expenses are payed on the first of each month. These will be gate rental, aircraft maintenance and, if you have them, lease rates. It's normal for your airline value to go down at the start of each month. Again, look at the finances page. If your "month to date" totals are negative but projected totals are in the black, you should be alright.
Now, I'd like to comment on your strategy so far. Perhaps you are making the same "mistakes" most of us did when we started playing (I know I did). You had two routes already established and quit those to set a couple more at somewhat high frequencies. When you offer fewer seats on a route you will be able to charge higher fares. If, instead of flying 3x daily to Palembang and 2.5x to Yogyakarta you would stay at 1x frequency on each route, you could raise your prices and set up new routes with the same plane. You might be serving a similar number of pax but, since they would be paying you higher, your profits would probably go up.
P.S. - You still keep 2 gates at Jakarta but are using only one (each gate is good for 10 slots or frequencies). Unless you're planning on using the extra capacity very soon, you'd better give back one of the gates. This way, you won't be paying for the unused capacity. Just don't do it if you're planning on using the gate in the next month, otherwise you would be renting it again, paying the same.
