Suricata

When running suricata processing a pcap file, I see different alerts between runmode=autofp and runmode=single.
Some of the differences could be thresholds, but for sid:2221010, which have apps-layer-event, but no thresholds, I still see differences.

The attached script runs suricata on a specific pcap file with a specified runmode. To run the two cases, I do:
./test-one-file LL1999_Week1_Tue_inside.pcap single
./test-one-file LL1999_Week1_Tue_inside.pcap autofp

Comparing the results, there are different number of alerts for sid:2221010
grep 1:2221010:1 single-results/LL1999_Week1_Tue_inside.sorted | wc -l
4694
ken@lab-39:~/test-suricata$ grep 1:2221010:1 autofp-results/LL1999_Week1_Tue_inside.sorted | wc -l
4373

Test pcap file: http://www.ll.mit.edu/mission/communications/cyber/CSTcorpora/ideval/data/1999/training/week1/tuesday/inside.tcpdump.gz

git version: c1190545cfb1d06037847b94620591d2be6f3c07

$ LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/suricata --build-info
This is Suricata version 2.0dev (rev c119054)
Features: PCAP_SET_BUFF LIBPCAP_VERSION_MAJOR=1 AF_PACKET HAVE_PACKET_FANOUT LIBCAP_NG LIBNET1.1 HAVE_HTP_URI_NORMALIZE_HOOK
64-bits, Little-endian architecture
GCC version 4.6.3, C version 199901
__GCC_HAVE_SYNC_COMPARE_AND_SWAP_1
__GCC_HAVE_SYNC_COMPARE_AND_SWAP_2
__GCC_HAVE_SYNC_COMPARE_AND_SWAP_4
__GCC_HAVE_SYNC_COMPARE_AND_SWAP_8
__GCC_HAVE_SYNC_COMPARE_AND_SWAP_16
compiled with -fstack-protector
compiled with _FORTIFY_SOURCE=2
L1 cache line size (CLS)=64
compiled with LibHTP v0.5.7, linked against LibHTP v0.5.7
Suricata Configuration:
AF_PACKET support: yes
PF_RING support: no
NFQueue support: no
IPFW support: no
DAG enabled: no
Napatech enabled: no
Unix socket enabled: no

libnss support:                          no
  libnspr support:                         no
  libjansson support:                      no
  Prelude support:                         no
  PCRE jit:                                no
  libluajit:                               no
  libgeoip:                                no
  Non-bundled htp:                         no
  Old barnyard2 support:                   no
  CUDA enabled:                            no

Suricatasc install:                      yes

Unit tests enabled:                      no
  Debug output enabled:                    no
  Debug validation enabled:                no
  Profiling enabled:                       no
  Profiling locks enabled:                 no

Generic build parameters:
Installation prefix (--prefix): /usr/local
Configuration directory (--sysconfdir): /usr/local/etc/suricata/
Log directory (--localstatedir) : /usr/local/var/log/suricata/

Host:                                    x86_64-unknown-linux-gnu
  GCC binary:                              gcc
  GCC Protect enabled:                     no
  GCC march native enabled:                yes
  GCC Profile enabled:                     no

CPU (12 cores 2 threads/core):
processor : 23
vendor_id : GenuineIntel
cpu family : 6
model : 44
model name : Intel(R) Xeon(R) CPU X5660 @ 2.80GHz
stepping : 2
microcode : 0xc
cpu MHz : 2793.017