Things I would check/try:
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make sure that the permissions on the App_Data folder are still correct, that is where it will upload temporary files until the upload completes by default, but if it is not writable then it uses Windows\TEMP and this could be outside your allocated disk space and may have different limits
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try increasing the setting for maxNormalRequestLength in the NeatUpload settings.
Understand that if you disable NeatUpload then those settings no longer apply and the settings from the <httpRuntime element are used instead as mentioned in the documentation.
If it was working for a while then this problem began to occur and no changes to the installation have been made then something has changed in server configuration. These settings can be controlled by machine.config and can override settings in Web.config, there could also have been a request filtering module enabled on the server and that may implement its own limits on requests separate from the normal settings.
Hope it helps,
Joe