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Yes, your WAN slowness might be mostly due to WAN latency.
Often network applications are written very interactively and the additional latency, on WAN, can slow them greatly compared to LAN, where latency is often sub millisecond.
Your "regular windows copies are fast" likely because bulk data transfers have "windowing" which allows them to sometimes (eventually) copy as fast as they will on a LAN. (If the Windows file copy, though, shows current transfer rate, you might notice the initially transfer rate takes a longer to get to full speed on the WAN vs. a LAN. If you do, that's also because of WAN latency.)
Your latest post also mention IPSec and SSL VPN. These too can slow things down a bit. One notable potential issue is packet fragmentation for encrypted packets; this may, or may not, be happening on your database application. Fragmentation generally only happens on nearly full sized packets.
