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Context: Grandad was bought food as a gift for looking after Maruko. Maruko
apologises to grandad because dad has just eaten it all. Then Grandad says:

> 「いいんじゃよ、まる子。おじいちゃんは別にただまる子をかわいがっているだけじゃ」  
>  Grandad (I) just cares for Maruko.

I'm familiar with 別に when used in a negative clause to mean "(not)
particularly". I can't understand what it means in this sentence.

Also a bit confused about the placement of だけ. If it's at the end doesn't it
mean that he does nothing but care for Maruko i.e. "All I do is care for just
(ただ) Maruko".

If it helps, the previous sentence is

> 「おじいちゃん、おばあちゃん、ごめんね」

which is said by Maruko.
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grammar
別に in non-negative clause
I think I was over-complicating my earlier attempts at an answer.

別に does not have to be with an explicit negative.

For example: 「別にいいけど」 might be roughly "different from (what you might expect
I don't have any strong feelings).. but it is okay (I guess)".

It's role is to separate and contrast. 別 means "different"/"separate" after
all. In particular, 別に often means "different from what you might be
expecting". It often denotes a level of indifference. ("maybe you expected me
to have a strong opinion, but different from your expectation, I actually feel
meh about it"). The following link has a more detailed explanation, and many
examples (some with no explicit negative)

<http://www.guidetojapanese.org/blog/2006/09/01/i-was-going-to-make-a-better-
title-but-eh-whatever/>

In this case, maybe the most straight-forward reading is "It is okay, Maruko.
(I don't particularly mind about that), I am simply (happy to) just dote on
you."
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> 「いいんじゃよ、まる[子]{こ}。おじいちゃんは[別]{べつ}にただまる子をかわいがっているだけじゃ。」

There is nothing wrong or unnatural about this as a **_casual spoken line_**.
You really should not apply the rigid grammar required for formally written
Japanese.

That said, I am actually "seeing" **_physically_** the negative element with
which 「別に」 can be used quite naturally. This might surprise you, but I see it
in 「いいんじゃよ、まる子。」 = " ** _No problem!_** " That was said in response to
something Maruko had done or said, correct? Grandad has negated Maruko's
apology, and he now has all the reasons to use 「別に」.

> "No problem, Maruko! I just adore you for who you are. (It is as simple as
> that)."

(A literal TL is difficult as the line is completely colloquial.)

Finally, regarding the use of both 「ただ」 and 「だけ」, it is not uncommon that we
use them together in informal speech.
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This 別に still implies "not in particular", "nothing special". By saying 別に,
basically おじいちゃん wanted to say that she had no particular reason to feel
sorry, that there was nothing particularly wrong among them, etc.

I don't want to call this sentence perfectly well-formed, but such a sentence
can be heard in speech.

Aside from the meaning of "separately" which is totally different, you will
sometimes encounter 別に without explicit negative expressions. Depending on the
context, 別に implies various things, for example, "it's not a big issue, but
...", "nothing special, but ...", "I'm not particularly interested, but ...",
"meh", "no problem", "don't take it too seriously", etc.
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I am not going to go into the grammar etc, but will try to explain why and
what it does for statement.

> 「いいんじゃよ、まる子。おじいちゃんは別にただまる子をかわいがっているだけじゃ」

The 「別に」in this sentence really is not needed, but from the statement from
Maruko that she was sorry, it seems like the writer put it in to convey or add
some more feeling to Maruko that an apology is not necessary. Eg,

> 「別にいいよ」 Loosely translated as [Its Ok, I don't mind]

This part where 「ただ」is used.

> 「おじいちゃんは **別にただ** まる子を」
>
> Could be written like this and serve the same meaning, even without the 「別に」
>
> 「おじいちゃんは **ただ** 」
>
> Translated, [I (Granddad) **just**....... (Maruko)]

So with the 「別に」in or out of the sentence the later part of the translation is
really much the same.

> I [Granddad] just adore you.
>
> 「いいんじゃよ、まる子。おじいちゃんは別にただまる子をかわいがっているだけじゃ」
>
> So the overall translation to get the feeling of what Granddad is saying
> even though the first part basically just says [its OK, Maruko], adding the
> really inputs the feeling of what the「別に」adds to the sentence.:
>
> **Really** , its OK, Maruko. I [Granddad] just adore you.

The 「別に」just adds that feeling that Granddad **really** doesn't mind in the
Japanese version and really is quite hard to convey that feeling into a
literal English translation.

EDIT, I wrote this a few hours ago, but had a work issue to deal with, even
with all the good answers I will post anyway.
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