Check your acquisition settings, depending on the timebase and memory settings, a scope will often reduce the sample rate to improve update rate if left to its own settings.
Your scope seems to only have one ADC, as well, so if you have more than one channel enabled, your maximum sample rate will be lower. The MSO5000 series can do 8GS/s on one channel, 4GS/s on two, and 2GS/s on all four, so if you have a second channel enabled, even if there's no signal connected, your maximum sample rate will be only 4GS/s.