GPIB data and control (handshaking, attention, interrupt, etc) lines all float high and are driven low, using open-collector type drivers. (There are some exceptions, with certain "newer" instruments that support high speed signalling and use Tri-state drivers which drive the data bus high and low). The high signal level is created entirely through a termination network on each connected instrument that is nominally a 3.1K pull-up (to 5 V) and 6.2k pull-down resistor to ground. This creates a nominally 3.3 V signal on the line when floating. The signal levels are TTL, so a "high" is anything over 2.0 V. A low should be below 0.8 V. (It's worth noting that GPIB uses negative logic on all lines, so > 2.0 VDC is interpreted as 0/false, not 1/true).
If you have multiple unpowered devices, then the pull-up resistors are not pulling the bus to 5 V, but dragging it down to 0 V instead. This results in the floating signal level falling below the logic high threshold. This problem is made worse by the lack of proper GPIB drivers (with TTL level inputs) on the prologix adapter.
You may be able to work around the issue by installing extra pull-ups on the prologix controller. Maybe around 1 K, connected to 5V. Add these to the 8 data lines, and all 8 control signals (DAV, NRFD, NDAC, ATN, IFC, REN, SRQ, EOI). This is pins 1 to 11 and 13 to 17 on the GPIB connector.