You have 2 problems:
1) The LEDs started bright then dimmed because you didn't use a current-limiting resistor. So the current through the LEDs was way beyond their max rating which caused them to overheat and reduce their brightness as they got hotter and hotter. They might not feel hot on the outside, but inside they are burning.
The high current was also way beyond the battery's rating and caused its voltage to quickly run down.
2) Now some LEDs are brighter than others. They are all getting the same current when in series. So the dim ones now were damaged more by the previous over-current. Maybe the ones with more damage were located above the others. Hot air rises.