diff --git a/tests/fate-run.sh b/tests/fate-run.sh
index 0165812208..1a8ff940bd 100755
--- a/tests/fate-run.sh
+++ b/tests/fate-run.sh
@@ -229,20 +229,17 @@ gapless(){
     decfile3="${outdir}/${test}.out-3"
     cleanfiles="$cleanfiles $decfile1 $decfile2 $decfile3"
 
-    # large enough to make ffmpeg.c seek to the start of the file
-    start_offset=-1
-
     # test packet data
-    ffmpeg -i "$sample" $extra_args -flags +bitexact -c:a copy -f framecrc -y $decfile1
+    ffmpeg $extra_args -i "$sample" -flags +bitexact -c:a copy -f framecrc -y $decfile1
     do_md5sum $decfile1
     # test decoded (and cut) data
-    ffmpeg -i "$sample" $extra_args -flags +bitexact -f wav md5:
+    ffmpeg $extra_args -i "$sample" -flags +bitexact -f wav md5:
     # the same as above again, with seeking to the start
-    ffmpeg -ss $start_offset -i "$sample" $extra_args -flags +bitexact -c:a copy -f framecrc -y $decfile2
+    ffmpeg $extra_args -ss 0 -seek_timestamp 1 -i "$sample" -flags +bitexact -c:a copy -f framecrc -y $decfile2
     do_md5sum $decfile2
-    ffmpeg -ss $start_offset -i "$sample" $extra_args -flags +bitexact -f wav md5:
+    ffmpeg $extra_args -ss 0 -seek_timestamp 1 -i "$sample" -flags +bitexact -f wav md5:
     # test packet data, with seeking to a specific position
-    ffmpeg -ss 5 -i "$sample" $extra_args -flags +bitexact -c:a copy -f framecrc -y $decfile3
+    ffmpeg $extra_args -ss 5 -seek_timestamp 1 -i "$sample" -flags +bitexact -c:a copy -f framecrc -y $decfile3
     do_md5sum $decfile3
 }
 
diff --git a/tests/ref/fate/gapless-mp3 b/tests/ref/fate/gapless-mp3
index 3cff9a86f9..984ae8489d 100644
--- a/tests/ref/fate/gapless-mp3
+++ b/tests/ref/fate/gapless-mp3
@@ -1,5 +1,5 @@
 d5c88cf38416329a052a9b0cb140fb4c *tests/data/fate/gapless-mp3.out-1
 c96c3ae7bd3300fd2f4debac222de5b7
-68f040b12d79c71e3b2e8ba90a9cbd96 *tests/data/fate/gapless-mp3.out-2
+3386bc2009b31b7ef39247918cbb02a5 *tests/data/fate/gapless-mp3.out-2
 c96c3ae7bd3300fd2f4debac222de5b7
-e750fc8ae00ba29a03983edafbb63975 *tests/data/fate/gapless-mp3.out-3
+70e7cd7f2b6365e7f48ed206113f06fc *tests/data/fate/gapless-mp3.out-3
diff --git a/tests/ref/fate/gapless-mp3-notoc b/tests/ref/fate/gapless-mp3-notoc
index 3528e71f96..f52efff249 100644
--- a/tests/ref/fate/gapless-mp3-notoc
+++ b/tests/ref/fate/gapless-mp3-notoc
@@ -1,5 +1,5 @@
 d5c88cf38416329a052a9b0cb140fb4c *tests/data/fate/gapless-mp3-notoc.out-1
 c96c3ae7bd3300fd2f4debac222de5b7
-68f040b12d79c71e3b2e8ba90a9cbd96 *tests/data/fate/gapless-mp3-notoc.out-2
+3386bc2009b31b7ef39247918cbb02a5 *tests/data/fate/gapless-mp3-notoc.out-2
 c96c3ae7bd3300fd2f4debac222de5b7
-e750fc8ae00ba29a03983edafbb63975 *tests/data/fate/gapless-mp3-notoc.out-3
+e82eaed507ce3f7f6199918159e1ddd7 *tests/data/fate/gapless-mp3-notoc.out-3