Ok so it seems like this issue only exists in Horizontal Mode A (and ALT obviously to the extent A is involved with ALT) However when in B mode the scope works fine with no issues. Id hope this would narrow down the cause, the movie below elaborates on the issue.
https://youtu.be/lTkdPYGIRRUApparently This setting deals with which sweep generator is used (page 2-6 of the operators manual)
I believe sweep generator A is BLOCK 3 of the block diagram which may be disassociated with Alternate B in BLOCK 5
From TM 11-6625-3135-40 page 1-4
Al MAIN CIRCUIT BOARD ASSEMBLY (C) — Provides instrument working voltages and processes vertical and horizontal signals.
A5 ALTERNATE SWEEP CIRCUIT BOARD ASSEMBLY (D) — Processes Alternate B Sweep horizontal signals.
From TM 11-6625-3135-40 page 1-8
A Sweep Generator and Logic Circuit (fig. FO-8)
Alternate Sweep Logic Circuit (fig. FO-9)
A SWEEP GENERATOR AND LOGIC CIRCUIT. The A sweep generator logic circuit controls A Sweep generation and Z-Axis unblinking. When the A TRIGGER mode switches are set to either P-P AUTO or TV FIELD (with no trigger signal present), a reference sweep is produced. In the NORM setting, sweeps are inhibited until a trigger input is present. This is useful for low-repetition-rate triggering. The SGL SWP setting allows only one sweep at a time to be generated. The sweep signal is applied to the horizontal amplifier.
ALTERNATE SWEEP LOGIC CIRCUIT. The alternate sweep logic circuit controls the alternate and B horizontal mode displays, intensity, Z-Axis amplifier drive level, and includes the B Miller sweep generator and B sweep logic circuitry. It also provides the B sweep sawtooth waveform and generates signals to control switching between the A and B displays.
From TM 11-6625-3135-40 page 2-21
Monitor A4R701 (161) pin 1 for approximately -8 vdc ±50 mv, as switch is turned through all TIMING ranges. ? If voltage varies more than 5 mV, replace A4 (para 2-20).
From TM 11-6625-3135-40 page 2-47
A4 TIMING CIRCUIT BOARD ASSEMBLY REPLACEMENT