Yes. There is a size limitation caused by Microsoft Search Service.
Foxit PDF IFilter does not have any size restriction of the PDF and neither does the evaluation version.
You can change the size limitation in the registry if needed.
For SharePoint Server
Please refer to http://support.microsoft.com/default.aspx?scid=kb;EN-US;318747.
For Sharepoint 2010
Execute the following steps on the SharePoint 2010 PowerShell console:
1) Get the Search Service Application and store it in a variable by running:
$ssa = Get-SPEnterpriseSearchServiceApplication
2) Get the current value of the MaxDownloadSize in the MSSConfiguration table by running:
3) Get the current value of the MaxGrowFactor in the MSSConfiguration table by running:
4) Modify the MaxDownloadSize and MaxGrowFactor values (assuming the customer wants or needs to adjust MaxGrowFactor) by running:
For Desktop Environment
Locate the following key in the registry and change its value.
HKEY_LOCAL_MACHINESOFTWAREMicrosoftWindows SearchGathering ManagerMaxDownloadSize
HKEY_LOCAL_MACHINESOFTWAREMicrosoftWindows SearchGathering ManagerMaxGrowFactor
To make the changes take effect, it will require a restart of your search services.
On Desktop, you just need to restart the computer and rebuild the index from Start > Control Panel > Indexing Options.
On SharePoint Server, it requires you to do an IISreset, stop and restart search service.