We believe this may be related to or a duplicate of the issue mentioned in: viewtopic.php?t=16496. Another member of our team requested assistance with the same issue almost a year ago: viewtopic.php?t=27641, but was unable to find a solution. At the time we resorted to simply reprocessing images with the symptom but that is no longer a viable solution.
Our current platform is Centos 7 running in the Amazon EC2 environment. We have installed numerous different versions of ImageMagick and have determined that version 6.7.4-4 is the last version where we do not observe the problem. Note that 6.7.4-4 will not build on Centos 7 due to incompatibility with the version of zlib. So, part of the experiment was performed on a Centos 6.5 server specifically dedicated to troubleshooting this problem. We have verified though that the line problem is consistent between later versions of ImageMagick regardless of whether the OS is Centos 6.5 or 7.
Interestingly we also noted a decrease in performance in all versions after 6.7.3-3. Our processing sequence consistently took 3 to 5 seconds in 6.7.3-3 and 17 to 20 seconds in 6.7.3-4 and later. This may or may not be related but seems like it is worth a mention.
Currently we have a Centos 7 server setup with ImageMagick 6.9.3-8 and we can reproduce the issue by running the following command up to 1000 times:
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convert -limit map 512mb -limit memory 512mb -limit thread 1 -size '2000x2000' -quality 85 -flatten -scale '2000x2000' '1000.jpg' $filePart1$i$fileExt;