vp9: update timestamps in ref files using multiple invisible frames.

For the 10-show-existing-frame, the source file indeed has a timestamp
of 3 (or 100/33) for the second visible frame, so the fix appears to
work correctly. For the other, only the timebase is fixed, but again
appears to be correct now.

tests/ref/fate/vp9-10-show-existing-frame

@@ -4,7 +4,7 @@
 #tb 0: 1/30
 #stream#, dts,        pts, duration,     size, hash
 0,          0,          0,        1,   152064, 18981342ec178e082519451062c3a67f
-0,          1,          1,        1,   152064, 04ab9dbeac49ec31be58f6e671698e05
+0,          3,          3,        1,   152064, 04ab9dbeac49ec31be58f6e671698e05
 0,          4,          4,        1,   152064, 4ed58a0ba93a5d97a232a50c5876cda2
 0,          6,          6,        1,   152064, a41f00034923e56ba51a0b598acc2e3a
 0,          7,          7,        1,   152064, 63fa55ae9535ccdf06d44cce8065dda6

tests/ref/fate/vp9-16-intra-only

 #format: frame checksums
 #version: 1
 #hash: MD5
-#tb 0: 12/359
+#tb 0: 1001/30000
 #stream#, dts,        pts, duration,     size, hash
 0,          0,          0,        1,   152064, d57529601178948afa4818c3c8938884
 0,          1,          1,        1,   152064, d47e00250c45733d64af067a417bcd06