Very well could come from l2bin -- any good way to determine that? I perfomed l2bin on each file individually, then l3 bin in chunks of 8 days worth of files. Finally l3mapgen. Here's an image of my l3mapgen parameters:

Here's a link to the final L3 mapped file:
https://www.dropbox.com/s/w70ek5g9te9a653/A2016193-200_8D_L3M.nc?dl=0And a link to the L3 bin file:
https://www.dropbox.com/s/kuegkcahaeh3cxg/A20161932016200.L3b_8D_SST?dl=0Here's the log file readout for one instance of using l3bin:
And below that, I've posted the l3mapgen log.
Thanks!
Execution log for
[/Applications/seadas-7.3.2/ocssw/run/scripts/ocssw_runner, --ocsswroot, /Applications/seadas-7.3.2/ocssw, l3bin, parfile=/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_SST/L3_Binned/Jul_11-13/tmpParFile2681278049870431981.par]
L3BIN 4.20 (Apr 27 2016 10:27:28)
66 input files
0 A2016193121000.L3b_DAY_SST.nc
1 A2016193134500.L3b_DAY_SST.nc
2 A2016193135000.L3b_DAY_SST.nc
3 A2016193200500.L3b_DAY_SST.nc
4 A2016193201000.L3b_DAY_SST.nc
5 A2016193214500.L3b_DAY_SST.nc
6 A2016193215000.L3b_DAY_SST.nc
7 A2016193232000.L3b_DAY_SST.nc
8 A2016193232500.L3b_DAY_SST.nc
9 A2016194111500.L3b_DAY_SST.nc
10 A2016194125000.L3b_DAY_SST.nc
11 A2016194125500.L3b_DAY_SST.nc
12 A2016194191500.L3b_DAY_SST.nc
13 A2016194205000.L3b_DAY_SST.nc
14 A2016194205500.L3b_DAY_SST.nc
15 A2016194222500.L3b_DAY_SST.nc
16 A2016194223000.L3b_DAY_SST.nc
17 A2016195000500.L3b_DAY_SST.nc
18 A2016195001000.L3b_DAY_SST.nc
19 A2016195115500.L3b_DAY_SST.nc
20 A2016195133500.L3b_DAY_SST.nc
21 A2016195195500.L3b_DAY_SST.nc
22 A2016195213000.L3b_DAY_SST.nc
23 A2016195213500.L3b_DAY_SST.nc
24 A2016195231000.L3b_DAY_SST.nc
25 A2016195231500.L3b_DAY_SST.nc
26 A2016196124000.L3b_DAY_SST.nc
27 A2016196203500.L3b_DAY_SST.nc
28 A2016196204000.L3b_DAY_SST.nc
29 A2016196221500.L3b_DAY_SST.nc
30 A2016196222000.L3b_DAY_SST.nc
31 A2016196235000.L3b_DAY_SST.nc
32 A2016196235500.L3b_DAY_SST.nc
33 A2016197114500.L3b_DAY_SST.nc
34 A2016197132000.L3b_DAY_SST.nc
35 A2016197132500.L3b_DAY_SST.nc
36 A2016197194500.L3b_DAY_SST.nc
37 A2016197212000.L3b_DAY_SST.nc
38 A2016197212500.L3b_DAY_SST.nc
39 A2016197225500.L3b_DAY.SST.nc
40 A2016197230000.L3b_DAY_SST.nc
41 A2016198122500.L3b_DAY_SST.nc
42 A2016198123000.L3b_DAY_SST.nc
43 A2016198140500.L3b_DAY_SST.nc
44 A2016198202500.L3b_DAY_SST.nc
45 A2016198203000.L3b_DAY_SST.nc
46 A2016198220000.L3b_DAY_SST.nc
47 A2016198220500.L3b_DAY_SST.nc
48 A2016198234000.L3b_DAY_SST.nc
49 A2016198234500.L3b_DAY_SST.nc
50 A2016199113000.L3b_DAY_SST.nc
51 A2016199131000.L3b_DAY_SST.nc
52 A2016199193000.L3b_DAY_SST.nc
53 A2016199193500.L3b_DAY_SST.nc
54 A2016199210500.L3b_DAY_SST.nc
55 A2016199211000.L3b_DAY_SST.nc
56 A2016199224500.L3b_DAY_SST.nc
57 A2016199225000.L3b_DAY_SST.nc
58 A2016200121500.L3b_DAY_SST.nc
59 A2016200135500.L3b_DAY_SST.nc
60 A2016200201000.L3b_DAY_SST.nc
61 A2016200201500.L3b_DAY_SST.nc
62 A2016200215000.L3b_DAY_SST.nc
63 A2016200215500.L3b_DAY_SST.nc
64 A2016200232500.L3b_DAY_SST.nc
65 A2016200233000.L3b_DAY_SST.nc
irow: 0 of 17280 Fri Jan 27 15:53:09 2017
...
irow: 17000 of 17280 Fri Jan 27 15:54:53 2017
L3mapgen log:
Execution log for
[/Applications/seadas-7.3.2/ocssw/run/scripts/ocssw_runner, --ocsswroot, /Applications/seadas-7.3.2/ocssw, l3mapgen, par=/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_SST/L3_Binned/Jul_11-18/tmpParFile6618878568457695416.par]
l3mapgen 1.0.1-r12911 (Apr 27 2016 10:21:34)
ifile : /Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_SST/L3_Binned/Jul_11-18/A20161932016200.L3b_8D_SST
ofile : /Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_SST/L3_Binned/Jul_11-18/output
oformat : netcdf4
projection : platecarree
resolution : 1159.578m
product : sst,qual_sst,flags_sst,bias_sst,stdv_sst,sstref
north : 61.995
south : 44.005
east : -122.409
west : -149.999
image size : 1727 x 2648
1% complete
...
99% complete
actual data min : 0.000000
actual data max : 23356.000000
num filled pixels : 873205
percent filled pixels : 19.09%