Issue 1:
julia> Pkg.checkout("DataStreams", "0.0.6")
INFO: Checking out DataStreams 0.0.6...
ERROR: GitError(Code:ERROR, Class:Merge, There is no tracking information for the current branch.)
in #123 at .\libgit2\libgit2.jl:414 [inlined]
in with(::Base.LibGit2.##123#128{Base.LibGit2.GitRepo}, ::Void) at .\libgit2\types.jl:638
in (::Base.LibGit2.##119#124{String,String,Bool,Base.LibGit2.MergeOptions,Base.LibGit2.CheckoutOptions,Base.LibGit2.GitRepo})(::Base.LibGit2.GitReference) at .\libgit2\libgit2.jl:412
in with(::Base.LibGit2.##119#124{String,String,Bool,Base.LibGit2.MergeOptions,Base.LibGit2.CheckoutOptions,Base.LibGit2.GitRepo}, ::Base.LibGit2.GitReference) at .\libgit2\types.jl:638
in (::Base.#kw##merge!)(::Array{Any,1}, ::Base.#merge!, ::Base.LibGit2.GitRepo) at .\<missing>:0
in (::Base.Pkg.Entry.##18#20{String,String,Bool,Bool})(::Base.LibGit2.GitRepo) at .\pkg\entry.jl:231
in transact(::Base.Pkg.Entry.##18#20{String,String,Bool,Bool}, ::Base.LibGit2.GitRepo) at .\libgit2\libgit2.jl:520
in with(::Base.Pkg.Entry.##17#19{String,String,Bool,Bool}, ::Base.LibGit2.GitRepo) at .\libgit2\types.jl:638
in checkout(::String, ::String, ::Bool, ::Bool) at .\pkg\entry.jl:227
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#checkout,Tuple{String,String,Bool,Bool}})() at .\pkg\dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#checkout,Tuple{String,String,Bool,Bool}}, ::String) at .\file.jl:48
in #cd#1(::Array{Any,1}, ::Function, ::Function, ::String, ::Vararg{Any,N}) at .\pkg\dir.jl:31
in checkout(::String, ::String) at .\pkg\pkg.jl:170

julia> Pkg.status()
6 required packages:
- ExcelReaders 0.6.0
- Gallium 0.0.3
- Lora 0.5.4
- Mimi 0.2.0
- NamedTuples 1.0.0
- TypedTables 0.1.1+ julia-0-5
59 additional packages:
- ASTInterpreter 0.0.3
- AbstractTrees 0.0.3
- ArgParse 0.3.1
- BinDeps 0.4.2
- COFF 0.0.1
- CRC 1.1.1
- Calculus 0.1.15
- CategoricalArrays 0.0.2
- ColorTypes 0.2.5
- Colors 0.6.6
- Compat 0.8.6
- Conda 0.2.3
- DWARF 0.0.3
- DataArrays 0.3.8
- DataFrames 0.7.4+ nl/nullable
- DataStreams 0.0.7 0.0.6
- DataStructures 0.4.5
- Dates 0.4.4
- Distributions 0.10.2
- DocStringExtensions 0.1.0
- Docile 0.5.23
- Documenter 0.2.0
- ELF 0.0.3
- FileIO 0.1.0
- FixedPointNumbers 0.1.4
- Formatting 0.1.5
- ForwardDiff 0.2.2
- FunctionWrappers 0.0.0- master (unregistered)
- GZip 0.2.20
- Graphs 0.6.0
- JSON 0.6.0
- JuliaParser 0.7.4
- LegacyStrings 0.1.1
- LibExpat 0.2.0
- MachO 0.0.3
- MacroTools 0.3.2 master
- NaNMath 0.2.1
- NullableArrays 0.0.7
- ObjFileBase 0.0.3
- PDMats 0.4.2
- PyCall 1.7.0
- Query 0.0.0- master (unregistered)
- Reactive 0.3.4
- Reexport 0.0.3
- ReverseDiffSource 0.2.3
- Rmath 0.1.2
- SHA 0.2.0
- SQLite 0.3.3+ master
- SortingAlgorithms 0.1.0
- StatsBase 0.9.0
- StatsFuns 0.3.0
- StructIO 0.0.2
- TerminalUI 0.0.2
- TextWrap 0.1.6
- URIParser 0.1.6
- VT100 0.0.2
- WeakRefStrings 0.1.2
- WinRPM 0.2.0
- Zlib 0.1.12

julia>

Looking at the repo itself, there also seems some data corruption, in particular the upstream info seems to be deleted:

C:\Users\anthoff\.julia\v0.5\DataStreams [0.0.6]> git status
On branch 0.0.6
Your branch is based on 'origin/0.0.6', but the upstream is gone.
(use "git branch --unset-upstream" to fixup)
nothing to commit, working directory clean
C:\Users\anthoff\.julia\v0.5\DataStreams [0.0.6]>

Issue 2:
Starting from a tagged version:

julia> Pkg.checkout("TaylorSeries", "warningsv05")
INFO: Checking out TaylorSeries warningsv05...
ERROR: GitError(Code:ERROR, Class:Merge, There is no tracking information for the current branch.)

but this works if master is checkouted first.