This pipeline:

gst-launch filesrc location=theora-skip-frames-test.y4m ! y4mdec ! theoraenc speed-level=4 bitrate=600 keyframe-freq=120 ! oggmux ! filesink location=out-600kbps.ogv

creates an output file where a bunch of frames are skipped.  encoder_example from the theora source does not exhibit this problem.  (speed-level=4 just makes it easier to spot.  It's there at the default speed-level.)  Note that this source *does* have duplicated frames, as it was converted from 24 to 30 fps.

Source is: http://www.schleef.org/~ds/theora-skip-frames-test.y4m

oggz-dump output:

00:00:09.200: serialno 1330046346, calc. gpos 257|20, packetno 279: 0 bytes
00:00:09.233: serialno 1330046346, calc. gpos 257|21, packetno 280: 10.502 kB
00:00:09.266: serialno 1330046346, calc. gpos 257|22, packetno 281: 375 bytes
00:00:09.300: serialno 1330046346, granulepos 257|23, packetno 282: 0 bytes
00:00:09.333: serialno 1330046346, calc. gpos 257|24, packetno 283: 0 bytes
00:00:09.366: serialno 1330046346, calc. gpos 257|25, packetno 284: 0 bytes
00:00:09.400: serialno 1330046346, calc. gpos 257|26, packetno 285: 10.744 kB
00:00:09.433: serialno 1330046346, granulepos 257|27, packetno 286: 385 bytes
00:00:09.466: serialno 1330046346, calc. gpos 257|28, packetno 287: 5.616 kB
00:00:09.500: serialno 1330046346, calc. gpos 257|29, packetno 288: 0 bytes