With a right-click on the time ruler you get a pop-up menu with the menu item "Create marker here", "Set as Zero", "Disable mouse hover marker". Selecting the menu item "Create marker here" doesn't display the marker. But the marker is indeed set, but at another position. That displacement is dependent on the current display time resolution. 

Example: 
ticks every 20ms, units every 100ms, displacement: +24:20:31:23
ticks every 2s, units every 10s, displacement: +2149:21:48:11

This is reproducible, to make the marker visible you need to click on "Zoom out" about 38 times.

I observed this with PulseView 0.4.1 as well as with the nightly build:

$ ./pulseview -V
PulseView 0.5.0-git-f058e27

Libraries and features:
  PulseView 0.5.0-git-f058e27
  Qt 5.7.1
  glibmm 2.42.0
  Boost 1_60
  libsigrok 0.6.0-git-ea7a83a/4:0:0 (rt: 0.6.0-git-ea7a83a/4:0:0)
   - glib 2.44.1 (rt: 2.44.1/4401:1)
   - libzip 1.5.1
   - libserialport 0.1.1/1:0:1 (rt: 0.1.1/1:0:1)
   - libusb-1.0 1.0.20.11003-rc3 API 0x01000104
   - libftdi 1.2
   - Host i686-w64-mingw32.static.posix, little-endian
   - SCPI backends TCP, serial, USBTMC
  libsigrokdecode 0.6.0-git-30d27bd/4:0:0 (rt: 0.6.0-git-30d27bd/4:0:0)
   - glib 2.44.1 (rt: 2.44.1/4401:1)
   - Python 3.4.4 / 0x30404f0 (API 1013, ABI 3)
   - Host i686-w64-mingw32.static.posix, little-endian