OK, I hate to be a pain, but the problem is back and nothing has changed on the server that I know of. I now can't upload a slightly larger zip file (219MB). My previous tests were at 184MB (which still works fine).

If I use the OliverHine upload, it uploads the file to the windows file system, but doesn't show up in File Manager (no errors anywhere, just doesn't work).
If I copy it into the folder with Windows Explorer and then Synchronize in File Manager, it doesn't show up (again, no errors, just doesn't work).
If I upload it using File Manager, I get this out of memory error (even after a fresh reboot, my server has 4GB, 2GB pagefile, and only 700MB is in use after the reboot)

AssemblyVersion: 5.5.1
PortalID: 3
PortalName: Sopheon Product Support
UserID: 1
UserName: host
ActiveTabID: 458
ActiveTabName: File Manager
RawURL: /support/Admin/FileManager/tabid/458/ctl/Edit/mid/1592/ftype/File/rtab/458/Default.aspx
AbsoluteURL: /Default.aspx
AbsoluteURLReferrer: https://www.sopheon.com/support/Admin/FileManager/tabid/458/ctl/Edit/mid/1592/ftype/File/rtab/458/Default.aspx
UserAgent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.2; Trident/4.0; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)
DefaultDataProvider: DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider
ExceptionGUID: 6e41d243-0319-4fdd-b980-ab34f83f5ecf
InnerException: Exception of type 'System.OutOfMemoryException' was thrown.
FileName:
FileLineNumber: 0
FileColumnNumber: 0
Method: System.Web.HttpRawUploadedContent..ctor
StackTrace:
Message: DotNetNuke.Services.Exceptions.PageLoadException: Exception of type 'System.OutOfMemoryException' was thrown. ---> System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown. at System.Web.HttpRawUploadedContent..ctor(Int32 fileThreshold, Int32 expectedLength) at System.Web.HttpRequest.GetEntireRawContent() at System.Web.HttpRequest.GetMultipartContent() at System.Web.HttpRequest.FillInFormCollection() at System.Web.HttpRequest.get_Form() at System.Web.HttpRequest.get_HasForm() at System.Web.UI.Page.GetCollectionBasedOnMethod(Boolean dontReturnNull) at System.Web.UI.Page.DeterminePostBackMode() at System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) --- End of inner exception stack trace ---
Source:
Server Name: CMS2

I have been fighting with DNN since upgrading from 5.01.01 and am my wits end trying to get the file system to recognize the larger files like it used to, right now it will not sync with anything larger than 200mb. Right now I am not even able to put a download to my own software on our site for download. I was hoping that the upgrade to 5.6 would fix the issue but sadly that was not the case. So I am very interested in any potential fix to this issue.

Yes the extensions are valid. A zip file with the size of right around 200Mb will show in the file manager but not a 456mb file even though they were both added at the same time in the same way. What is even stranger is that the large files that were on the site before the upgrade still show up in file manager but not new ones