Try to run it with some logging options and then paste content of file here.
Ok, it was a bit difficult getting log file as the default antminer S1 settings hides cgminers display. So had to kill process and run my own cgminer outputting to log file.
Ran it for 5 mins.
[2014-05-11 02:09:26] Started cgminer 4.3.2a
[2014-05-11 02:09:26] BitmainAntS1: detected ANT0
[2014-05-11 02:09:26] ANT0: bitmain_initialize() parse_rxstatus version(3) chain_num(2) fifo_space(
[2014-05-11 02:09:26] ANT0: bitmain_initialize() parse_rxstatus chain(0) asic_num=32 asic_status=ff
[2014-05-11 02:09:26] ANT0: bitmain_initialize() parse_rxstatus chain(1) asic_num=32 asic_status=ff
[2014-05-11 02:09:26] ANT0: bitmain_initialize() set_txconfig
[2014-05-11 02:09:26] ANT0: bitmain_initialize() succeeded
[2014-05-11 02:09:26] Probing for an alive pool
[2014-05-11 02:09:27] Pool 0 difficulty changed to 256
[2014-05-11 02:09:27] Network diff set to 1M
(5s):0.000 (1m):0.000 (5m):0.000 (15m):0.000 (avg):0.000h/s ^M [2014-05-11 02:09:30] Stratu
[2014-05-11 02:09:30] ANT0: bitmain_flush_work() queued=0
[2014-05-11 02:09:30] BitmainAntS1: send task new block 1 old(0)
[2014-05-11 02:09:31] Stratum from pool 0 requested work restart
[2014-05-11 02:09:31] ANT0: bitmain_flush_work() queued=0
[2014-05-11 02:09:31] BitmainAntS1: send task new block 2 old(1)
(5s):92.75G (1m):11.36G (5m):2.343G (15m):785.4M (avg):157.5Gh/s ^M [2014-05-11 02:09:32] A
(5s):154.6G (1m):25.31G (5m):5.372G (15m):1.809G (avg):174.4Gh/s ^M [2014-05-11 02:09:37] R
(5s):177.2G (1m):38.37G (5m):8.405G (15m):2.845G (avg):179.4Gh/s ^M [2014-05-11 02:09:42] R
[2014-05-11 02:09:46] Accepted c7babcae Diff 328/256 ANT 0
(5s):181.2G (1m):50.02G (5m):11.32G (15m):3.852G (avg):180.7Gh/s ^M [2014-05-11 02:09:52] R
(5s):173.3G (1m):59.68G (5m):13.97G (15m):4.782G (avg):178.6Gh/s ^M(5s):187.6G (1m):70.53G
(5s):188.6G (1m):79.59G (5m):19.73G (15m):6.827G (avg):181.9Gh/s ^M [2014-05-11 02:10:03] R
[2014-05-11 02:10:04] Rejected 8ddd0063 Diff 462/256 ANT 0 (Share above target.)
[2014-05-11 02:10:04] Accepted e312c1a3 Diff 289/256 ANT 0
(5s):194.1G (1m):88.93G (5m):22.65G (15m):7.878G (avg):183.7Gh/s ^M [2014-05-11 02:10:08] A
[2014-05-11 02:10:09] Accepted 93979222 Diff 444/256 ANT 0
[2014-05-11 02:10:09] Rejected db8e206e Diff 298/256 ANT 0 (Share above target.)
[2014-05-11 02:10:11] Rejected 99912a56 Diff 427/256 ANT 0 (Share above target.)
(5s):189.8G (1m):96.33G (5m):25.27G (15m):8.839G (avg):183.5Gh/s ^M [2014-05-11 02:10:12] R
(5s):186.6G (1m):103.0G (5m):27.82G (15m):9.784G (avg):183.1Gh/s ^M(5s):188.2G (1m):110.1G
(5s):179.2G (1m):115.4G (5m):32.96G (15m):11.72G (avg):183.3Gh/s ^M [2014-05-11 02:10:30] N
[2014-05-11 02:10:30] Stratum from pool 0 detected new block
[2014-05-11 02:10:30] ANT0: bitmain_flush_work() queued=0
[2014-05-11 02:10:30] BitmainAntS1: send task new block 3 old(2)
(5s):179.8G (1m):120.6G (5m):35.39G (15m):12.65G (avg):183.1Gh/s ^M(5s):177.9G (1m):125.4G
(5s):178.1G (1m):129.9G (5m):40.19G (15m):14.52G (avg):183.0Gh/s ^M(5s):181.1G (1m):133.8G
[2014-05-11 02:10:47] ANT0: bitmain_flush_work() queued=0
[2014-05-11 02:10:48] BitmainAntS1: send task new block 4 old(3)
[2014-05-11 02:10:49] Rejected 7d43d949 Diff 523/256 ANT 0 (Share above target.)
(5s):173.5G (1m):136.6G (5m):44.58G (15m):16.28G (avg):181.9Gh/s ^M [2014-05-11 02:10:52] R
(5s):179.9G (1m):140.2G (5m):46.82G (15m):17.19G (avg):181.8Gh/s ^M(5s):183.9G (1m):143.8G
[2014-05-11 02:11:17] ANT0: bitmain_flush_work() queued=0
[2014-05-11 02:11:17] BitmainAntS1: send task new block 5 old(4)
(5s):177.4G (1m):153.0G (5m):57.32G (15m):21.61G (avg):181.0Gh/s ^M [2014-05-11 02:11:22] R
[2014-05-11 02:11:24] Rejected bbe1cbee Diff 349/256 ANT 0 (Share above target.)
(5s):180.8G (1m):155.3G (5m):59.37G (15m):22.49G (avg):181.0Gh/s ^M [2014-05-11 02:11:29] R
(5s):176.6G (1m):157.0G (5m):61.31G (15m):23.34G (avg):180.9Gh/s ^M [2014-05-11 02:11:36] S
[2014-05-11 02:11:37] Pool 0 difficulty changed to 512
[2014-05-11 02:11:37] Network diff set to 8G
[2014-05-11 02:11:37] Stratum from pool 0 detected new block
[2014-05-11 02:11:37] ANT0: bitmain_flush_work() queued=0
(5s):160.2G (1m):157.0G (5m):63.13G (15m):24.20G (avg):179.9Gh/s ^M [2014-05-11 02:11:39] P
[2014-05-11 02:11:39] Rejected 9c7100ee Diff 419/256 ANT 0 (Job not found.)
[2014-05-11 02:11:41] Pool 0 stale share detected, submitting as user requested
[2014-05-11 02:11:41] Rejected 4285d4c5 Diff 985/256 ANT 0 (Job not found.)
[2014-05-11 02:11:42] BitmainAntS1: send task new block 6 old(5)
(5s):174.0G (1m):159.7G (5m):65.00G (15m):25.01G (avg):180.5Gh/s ^M [2014-05-11 02:11:45] S
[2014-05-11 02:11:45] ANT0: bitmain_flush_work() queued=0
This is using the binaries from here:
https://github.com/kanoi/cgminer-binaries/tree/master/AntS1Nicehash website says ~60% reject rate.
The only thing that comes to my mind is that this miner is modifying ntime. We don't allow modified ntimes, because we have no methods to evaluate whether modified ntime would be accepted by remote pool or not. There should be a way to force miner not to modify ntime; in fact, there is plenty of extranonce2 size so the ntime doesn't have to be modified. Guess that is the change compared to older miner.