Wanna upload the full code?

Well the problem with the sub( command seems like somewhere you are generating a decimal part and sub( can't have those. It has to be an integer. So I would advise using iPart( instead of int( because it can have weird effects in some situations, I don't remember what they are though.

As for that second thing with the storing to the variable thing I'm not sure I understand what you mean by nothing is happening. Like that one isn't getting stored to the variable when the variable equals six? Or something else?

Well maybe I'll try iPart, but int( seems to work well enough...

What I'm saying is that X does not increment properly (like not at all) when X=3 AND Y=1. works fine in all other cases, including when I do other things to X.

Here's the code (not including the key, I've changed that up with no results) (don't currently have access to a link cable):
:"ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890->Str3
:"CIPHER-KEY-36-LETTERS+NUMBERS->Str4
:Prompt Str1
:" ->Str5
:For(A,1,length(Str1),2)
:A-1->A
:Repeat B or A=length(Str1)
:A+1->A
:sub(Str1,A,1->Str1
:int(inString(Str4,Str2->B
:If not(B
:Str5+Str2->Str5
:End
:If B
:Then
:A->D
:If A=length(Str1)
:Str1+A->Str1
:A-1->A
:Repeat C or A+2=length(Str1
:A+1->A
:sub(Str1,A+1,1)->Str2
:int(inString(Str4,Str2->C
:End
:If not(C
:Then
:Str1+A->Str1
:int(inString(Str4,"A->C
:End
:int((B-1)/6->T
:int(6fPart((B-1)/6)+1->S
:int((C-1)/6->U
:int(6fPart((C-1)/6)+1->V
:If not(S=U and T=V)
:Then
:If T=V
:Then
:S+1-6(S=6)->S
:U+1-6(U=6)->U
:Else
:If S=U
:Then
:T+1-6(T=5)->T
:V+1-6(V=5)->V
:Else
:S+U->S
:S-U->U
:S-U->S
:End
:End
:6T+S->B
:6U+S->C
:End
:int(B->B
:Str5+sub(Str4,B,1)->Str5
:If A-D<0
:Str5+sub(Str1,D+1,A-D)->Str5
:int(C->C
:Str5+sub(Str4,C,1)->Str5
:End
:End
:Disp Str5

EDIT: just noticed I never use Str3

iPart( and int( have the same effect for positive numbers, so that's not it.

It looks to me like fPart( is not returning the right number.  Try this when it crashes:
Figure out which variable was being used (it's probably the bad one).
Go into the Solver ([Math] [0])
Type that variable into the equation
Scroll up or down (I forget which) and look at all the digits of precision the calc has.  Here you can see what's happening to these numbers.

Fix: put a round(......,0 around the statement with the fpart(.  (Ex: int(6fPart((B-1)/6)+1->S changes to round(6fPart((B-1)/6)+1,0->S)

and... what is the difference between int(...) and round(...,0)?  Also, int( did fix my crashing problems.

okay more info on what is going wrong:
 if one_number = 9
    that_number=8
    if the_other = 8
      the_other=7
    end
  else
    everything works
  end

and 7 can be a valid #. lulz fun.

PS: what does round(...,0) do? I've always avoided round...

 yay!!! it works!

but now I'm having problems parsing non-text characters...

EDIT: nvm, i fixed it Time for extensive testing!

EDIT2: who wants the first shot at cracking it?  

Kz1 pxn lhxm ztkq pf zhmjuewppr vppo ynssp2a.P

EDIT3: attached complete file and a readme 

wow. found a typo in the decryption code
also made a random key generator. (inspired by JustCause's Secure (Ish) Cipher)

this really is a somewhat modified version of the Playfair Cipher. instead of adding an 'X' or 'Q' between two equal letters, I just let them slide through.  This might be a bit of a security concern (although it makes it harder to identify as a playfair cipher), so to make it more secure, you can change that easily or encrypt, add a letter to the beginning, and encrypt again. (or even decrypt )

I'm not sure if this really deserves a project thread. I don't really plan on adding much more.

EDIT (before post): wow... I forget to rename the readme and get an error... then I fix it, it says I've already posted.  I go and look at it, there is no post there. I re-open the reply page, copy & paste the text and reselect the files (none of which have the same name as any others on this thread) and... it says there is already a file with that name.