Thanks to all who answered for the help, some more background specifics.
My system:
Intel Core i5-760 Lynnfield 2.8GHz LGA 1156 95W Quad-Core Desktop Processor (not overclocked at the moment)
G.SKILL Ripjaws Series 4GB (2 x 2GB) 240-Pin DDR3 SDRAM DDR3 1600 (PC3 12800)
OCZ Agility 2 OCZSSD3-2AGT90G 3.5" 90GB SATA II MLC Internal Solid State Drive (SSD)
EVGA 012-P3-1470-AR GeForce GTX 470 (Fermi) 1280MB 320-bit GDDR5 PCI Express 2.0 x16
Microsoft Windows 7 Ultimate 64-bit 1-Pack for System Builders - OEM
GIGABYTE GA-P55-USB3 LGA 1156 Intel P55 USB 3.0 ATX Intel Motherboard
I also have a 2TB data drive. I have over half the SSD drive empty, but I am using bitlocker. I am currently decrypting just to see if that is the issue. I operate out of a standard user account and Civ5 runs under those user credentials. Civ5 is installed on the SSD, the game files are in "%user%\My Documents\My Games\Sid Meier's Civilization 5\" which is also on the SSD. I run Civ5 in DirectX11 mode.
The game freeze (hiccup) happens whether I am playing in a window or full screen. I generally raise the Civ5 process priority to high but have not noticed this help the save game hiccup. The page file is not overly busy and Civ5 rarely takes more than 1.5gigs of memory.
I notice is most pronounced when playing Large+ worlds, small continents or archipelago worlds. It doesn't start to show until I have planted my fourth city. I do clean out my old save game files before starting a new game and I only autosave every 10 turns, keep last 4. CPU load does not peg, but Civ5 stops responding for a short period during all saves once the delay starts to manifest. There are no entries in the error logs and running procmon and resource monitor do not show any disk usage or cpu usage bottleneck.
If I play a continents or Pangaea game the effect is less. If I play on a standard sized world the effect is less. If I play small and not small continents or archipelago the effect never manifests (even on a long run culture or space victory). Changing the video settings has had no affect on the game. The game is not sluggish and the graphics are very good. It is only when saving, manually or auto that the game begins manifesting the "not responding" symptom. Once that starts. Any attempt to load a game from other than fresh start from the desktop will cause a crash of Civ5.
I have validated the cache files in Steam (and just did again), and it is fine). I have uninstalled then re-installed, no change.
Just to be clear, other than when the game is saving, the game is flying. When it starts cramping, it cramps hard and begins to crash. It always crashes on loading once this happens, unless loading from a fresh restart of the Civ5 application. When it is not saving, the machine barely breaks a sweat running the game even large/huge worlds with high graphic settings.