I contacted the owner of smallflags.com
and asked about the missing countries. He said they are slowly adding flags, but they could be rushed by ordering them custom in one of the following two ways:
1) Pay $45 set up fee + 3/patch, no minimum
2) Buy 20+ Patches, no set up fee
If anyone would like to band together for a bulk purchase, I need: Lithuania, Albania, Montenegro, Croatia, Slovenia.
p.s. Turkey and Czech Republic are available through the site now.