Level-shifter messing with other voltage rails
You would not be having these problems if you used a level-shifter IC such as this one (SN74LVC1T45): 



• Fully Configurable Dual-Rail Design Allows Each
  Port to Operate Over the Full 1.65-V to 5.5-V
  Power-Supply Range
• VCC Isolation Feature – If Either VCC Input Is at
  GND, Both Ports Are in the High-Impedance State


As well as properly handling the translation and isolation functions, it is
considerably faster than the sluggish pullup of the transistor method (sub 16ns in most cases, with a 15pF load). 10K and 15pF has a 150ns time constant.