I had exactly the same problem. 
Solved it by editing:  
C:\Users\[your username]\Saved Games\DCS\Config\Input\A-10C\joystick 
(I'm on win 8.1)   
Here I found the following file: 
Throttle - HOTAS Warthog {randon-nr}.diff.lua   
I edited:   
	["keyDiffs"] = { 
		["d563pnilu565cdnilvdnilvpnilvunil"] = { 
			["name"] = "HOTAS Boat Switch Forward", 
			["removed"] = { 
				[1] = { 
					["key"] = "JOY_BTN9", 
				}, 
			}, 
		}, 
		["d564pnilu565cdnilvdnilvpnilvunil"] = { 
			["name"] = "HOTAS Boat Switch Aft", 
			["removed"] = { 
				[0] = { 
					["key"] = "JOY_BTN10",   
By setting the "removed" part to 0, like so:   
	["keyDiffs"] = { 
		["d563pnilu565cdnilvdnilvpnilvunil"] = { 
			["name"] = "HOTAS Boat Switch Forward", 
			["removed"] = { 
				[1] = { 
					["key"] = "JOY_BTN9", 
				}, 
			}, 
		}, 
		["d564pnilu565cdnilvdnilvpnilvunil"] = { 
			["name"] = "HOTAS Boat Switch Aft", 
			["removed"] = { 
				[0] = { 
					["key"] = "JOY_BTN10",   
Worked like a charm, I have my boat switch back :) 
Would definitely say this is a bug of some sort. Had to do a reinstall the other day and suddenly I had this problem (never had it before)   
Hope it works for you too!