Hi, ebalci.
The waveform has become AC-coupled somehow. Looking the plot you supplied, I would judge the time constant to be about 16 ns (corresponding to about a 10 MHz -3 dB frequency). If the source and load are both 50 ohms, that indicates that the size of the AC-coupling capacitance is around 160 pF.
The user guide for the scope indicates that AC-coupling is not allowed in 50-ohm input impedance mode. Further, the 5421 is always DC-coupled at the output. Hence the principal possibilities are:
1) The 5421 is defective.
2) The 6034 is defective.
3) The cable is defective.
I can suggest a few possibilities to determine the source of the problem.
a) If you have another substitute for any of items 1, 2, or 3, try that in its stead. For instance, if you have another 1 MHz square-wave generator, connect it to the scope and see what the waveform looks like. (Of course, the scientific method dictates that you should change only one of these elements at a time.)
b) If you have no substitutes, try changing the amplitude of the square-wave (at 1 MHz, or any frequency where you see the distortion) to see if the waveform improves. The idea is to switch the gain-setting attenuators on the board. If that has an effect, the problem is probably with the 5421.
Hope this helps,
Ed L.