Die strafrekord is beskikbaar, behalwe dat die agtergrondondersoek duur.

behalwe dat means except that or except for the fact that. It introduces a clause that limits or qualifies the statement before it.

So the structure is:

• main statement: Die strafrekord is beskikbaar
• qualification: behalwe dat ...

Afrikaans also uses plain behalwe in other patterns, but behalwe dat is specifically used before a full clause.

Afrikaans very often forms compound nouns as a single word.

So:

• straf = punishment / criminal
• rekord = record

Together, strafrekord is one compound noun. This is very normal in Afrikaans. English often writes similar ideas as two words, but Afrikaans usually joins them.

die is the definite article in Afrikaans, meaning the.

In this sentence:

• die strafrekord = the criminal record
• die agtergrondondersoek = the background check/investigation

A useful thing for English speakers: Afrikaans uses die for both singular and plural definite nouns, so it does not change the way English does with the anyway, but unlike some languages, there is no separate masculine/feminine form.

beskikbaar means available. It is being used as a predicate adjective, just like in English:

• Die strafrekord is beskikbaar

That is the normal Afrikaans pattern:

• noun phrase + is
  • adjective

So beskikbaar is not a verb here; it is an adjective describing the subject.

It is another compound noun:

• agtergrond = background
• ondersoek = investigation / examination / check

Together, agtergrondondersoek means background investigation or background check.

Again, Afrikaans strongly prefers writing this kind of compound as one word.

duur can mean two different things in Afrikaans:

1. expensive

   • Dit is duur = It is expensive.

2. to last / take a long time

   • Die vergadering duur lank = The meeting lasts a long time.

That makes this sentence a little tricky, because duur could be understood in more than one way unless the wider context makes it clear.

Because after dat, Afrikaans normally puts the finite verb near the end of the clause.

If the intended meaning is that the background check is expensive, standard Afrikaans would normally be:

• behalwe dat die agtergrondondersoek duur is

Here is goes to the end because dat introduces a subordinate clause.

But if duur is being used as a verb meaning takes a long time / lasts, then:

• behalwe dat die agtergrondondersoek duur

can work, although many speakers would make it clearer by saying:

• behalwe dat die agtergrondondersoek lank duur

So the sentence as written is either:

• slightly incomplete if duur means expensive, or
• acceptable but a bit ambiguous if duur means takes a long time.

Yes. dat introduces a subordinate clause, and in Afrikaans subordinate clauses usually push the finite verb toward the end.

Compare:

• Main clause: Die agtergrondondersoek is duur.
• Subordinate clause: ... dat die agtergrondondersoek duur is.

That is a very important Afrikaans word-order pattern to learn.

The first part, Die strafrekord is beskikbaar, is fully natural.

The second part needs care:

• If the meaning is the background check is expensive, the more natural form is
  behalwe dat die agtergrondondersoek duur is.

• If the meaning is the background check takes a long time, a clearer version is
  behalwe dat die agtergrondondersoek lank duur.

So a native speaker might understand the original, but would probably want a clearer ending.

Yes, the comma is natural here. It separates the main clause from the following qualifying clause.

So this punctuation looks fine:

• Die strafrekord is beskikbaar, behalwe dat ...

It helps show that the second part is an added limitation or exception to the first part.